From c38626844287674bc98f18424bbd82e046d36d4b Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Thu, 15 Jun 2023 09:24:31 -0400 Subject: [PATCH] Delete PTL1.2831.out --- PTL1/Transcriptomes/Scripts/PTL1.2831.out | 31859 -------------------- 1 file changed, 31859 deletions(-) delete mode 100644 PTL1/Transcriptomes/Scripts/PTL1.2831.out diff --git a/PTL1/Transcriptomes/Scripts/PTL1.2831.out b/PTL1/Transcriptomes/Scripts/PTL1.2831.out deleted file mode 100644 index aaee3ca..0000000 --- a/PTL1/Transcriptomes/Scripts/PTL1.2831.out +++ /dev/null @@ -1,31859 +0,0 @@ - -The following have been reloaded with a version change: - 1) GCCcore/10.2.0 => GCCcore/8.3.0 - 2) GMP/6.2.0-GCCcore-10.2.0 => GMP/6.1.2-GCCcore-8.3.0 - 3) Python/3.8.6-GCCcore-10.2.0 => Python/3.7.4-GCCcore-8.3.0 - 4) SQLite/3.33.0-GCCcore-10.2.0 => SQLite/3.29.0-GCCcore-8.3.0 - 5) Tcl/8.6.10-GCCcore-10.2.0 => Tcl/8.6.9-GCCcore-8.3.0 - 6) XZ/5.2.5-GCCcore-10.2.0 => XZ/5.2.4-GCCcore-8.3.0 - 7) binutils/2.35-GCCcore-10.2.0 => binutils/2.32-GCCcore-8.3.0 - 8) bzip2/1.0.8-GCCcore-10.2.0 => bzip2/1.0.8-GCCcore-8.3.0 - 9) libffi/3.3-GCCcore-10.2.0 => libffi/3.2.1-GCCcore-8.3.0 - 10) libreadline/8.0-GCCcore-10.2.0 => libreadline/8.0-GCCcore-8.3.0 - 11) ncurses/6.2-GCCcore-10.2.0 => ncurses/6.1-GCCcore-8.3.0 - 12) zlib/1.2.11-GCCcore-10.2.0 => zlib/1.2.11-GCCcore-8.3.0 - - -The following have been reloaded with a version change: - 1) GCC/8.3.0 => GCC/10.3.0 - 2) GCCcore/8.3.0 => GCCcore/10.3.0 - 3) binutils/2.32-GCCcore-8.3.0 => binutils/2.36.1-GCCcore-10.3.0 - 4) bzip2/1.0.8-GCCcore-8.3.0 => bzip2/1.0.8-GCCcore-10.3.0 - 5) zlib/1.2.11-GCCcore-8.3.0 => zlib/1.2.11-GCCcore-10.3.0 - - - -Prepping Sr_rh_Emac_assembledTranscripts.fasta - - -There are 60195 contigs > 200 in Sr_rh_Emac_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Tx01_assembledTranscripts.fasta - - -There are 142089 contigs > 200 in Sr_rh_Tx01_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn13_assembledTranscripts.fasta - - -There are 150535 contigs > 200 in Sr_rh_Nn13_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Sspa_assembledTranscripts.fasta - - -There are 96071 contigs > 200 in Sr_rh_Sspa_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn06_assembledTranscripts.fasta - - -There are 145214 contigs > 200 in Sr_rh_Nn06_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Atps_assembledTranscripts.fasta - - -There are 10253 contigs > 200 in Sr_rh_Atps_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Bv01_assembledTranscripts.fasta - - -There are 208216 contigs > 200 in Sr_rh_Bv01_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Bv05_assembledTranscripts.fasta - - -There are 218559 contigs > 200 in Sr_rh_Bv05_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Gl03_assembledTranscripts.fasta - - -There are 251483 contigs > 200 in Sr_rh_Gl03_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Bv04_assembledTranscripts.fasta - - -There are 224949 contigs > 200 in Sr_rh_Bv04_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Gl01_assembledTranscripts.fasta - - -There are 8191 contigs > 200 in Sr_rh_Gl01_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Hhir_assembledTranscripts.fasta - - -There are 55856 contigs > 200 in Sr_rh_Hhir_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn02_assembledTranscripts.fasta - - -There are 138826 contigs > 200 in Sr_rh_Nn02_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Slin_assembledTranscripts.fasta - - -There are 37070 contigs > 200 in Sr_rh_Slin_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Emar_assembledTranscripts.fasta - - -There are 43809 contigs > 200 in Sr_rh_Emar_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Calb_assembledTranscripts.fasta - - -There are 75768 contigs > 200 in Sr_rh_Calb_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Rsp1_assembledTranscripts.fasta - - -There are 167000 contigs > 200 in Sr_rh_Rsp1_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn09_assembledTranscripts.fasta - - -There are 221270 contigs > 200 in Sr_rh_Nn09_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn10_assembledTranscripts.fasta - - -There are 140733 contigs > 200 in Sr_rh_Nn10_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn01_assembledTranscripts.fasta - - -There are 172554 contigs > 200 in Sr_rh_Nn01_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn12_assembledTranscripts.fasta - - -There are 136924 contigs > 200 in Sr_rh_Nn12_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Bv03_assembledTranscripts.fasta - - -There are 228384 contigs > 200 in Sr_rh_Bv03_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Hind_assembledTranscripts.fasta - - -There are 65043 contigs > 200 in Sr_rh_Hind_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn04_assembledTranscripts.fasta - - -There are 312525 contigs > 200 in Sr_rh_Nn04_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn08_assembledTranscripts.fasta - - -There are 198852 contigs > 200 in Sr_rh_Nn08_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn07_assembledTranscripts.fasta - - -There are 172565 contigs > 200 in Sr_rh_Nn07_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn11_assembledTranscripts.fasta - - -There are 129060 contigs > 200 in Sr_rh_Nn11_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn14_assembledTranscripts.fasta - - -There are 152790 contigs > 200 in Sr_rh_Nn14_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Gsp1_assembledTranscripts.fasta - - -There are 62212 contigs > 200 in Sr_rh_Gsp1_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Halb_assembledTranscripts.fasta - - -There are 100948 contigs > 200 in Sr_rh_Halb_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Bv06_assembledTranscripts.fasta - - -There are 143978 contigs > 200 in Sr_rh_Bv06_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Gl02_assembledTranscripts.fasta - - -There are 261586 contigs > 200 in Sr_rh_Gl02_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn05_assembledTranscripts.fasta - - -There are 128153 contigs > 200 in Sr_rh_Nn05_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Nn03_assembledTranscripts.fasta - - -There are 131998 contigs > 200 in Sr_rh_Nn03_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Esca_assembledTranscripts.fasta - - -There are 99293 contigs > 200 in Sr_rh_Esca_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Usac_assembledTranscripts.fasta - - -There are 133441 contigs > 200 in Sr_rh_Usac_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Bv02_assembledTranscripts.fasta - - -There are 236067 contigs > 200 in Sr_rh_Bv02_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - - - -Prepping Sr_rh_Gspa_assembledTranscripts.fasta - - -There are 22017 contigs > 200 in Sr_rh_Gspa_assembledTranscripts.fasta - - -Look for /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa.200bp.fasta - - -Next Script is: 2_Auto_rRNA_BvE.py -(Alternatively 2a_remove_rRNA.py followed by 2b_remove_Bact.py) - - -MERGE following files -CREATE a dictionnary of sequences - -Error in cross-plate contamination assessment: the ten-digit code Sr_rh_Gspa is not found in the conspecific names file. Please check that this file is correct and try again. - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn02.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn02.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.212s] -Masking queries... [0.336s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.137s] -Allocating buffers... [0s] -Loading reference sequences... [1.097s] -Masking reference... [0.717s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.306s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.233s] -Building query seed array... [0.09s] -Computing hash join... [0.113s] -Building seed filter... [0.008s] -Searching alignments... [0.148s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.24s] -Building query seed array... [0.095s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.134s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.25s] -Building query seed array... [0.099s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.144s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.215s] -Building query seed array... [0.085s] -Computing hash join... [0.095s] -Building seed filter... [0.008s] -Searching alignments... [0.139s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.214s] -Building query seed array... [0.085s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.121s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.239s] -Building query seed array... [0.102s] -Computing hash join... [0.094s] -Building seed filter... [0.006s] -Searching alignments... [0.13s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.255s] -Building query seed array... [0.105s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.127s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.092s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.126s] -Deallocating buffers... [0.057s] -Computing alignments... [1.45s] -Deallocating reference... [0.023s] -Loading reference sequences... [0s] -Deallocating buffers... [0.021s] -Deallocating queries... [0.012s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.975s -Reported 13195 pairwise alignments, 13268 HSPs. -13195 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.247s] -Masking queries... [0.318s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.128s] -Allocating buffers... [0s] -Loading reference sequences... [0.978s] -Masking reference... [0.649s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.27s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.218s] -Building query seed array... [0.101s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.324s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.224s] -Building query seed array... [0.104s] -Computing hash join... [0.088s] -Building seed filter... [0.008s] -Searching alignments... [0.278s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.234s] -Building query seed array... [0.097s] -Computing hash join... [0.089s] -Building seed filter... [0.008s] -Searching alignments... [0.261s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.195s] -Building query seed array... [0.086s] -Computing hash join... [0.09s] -Building seed filter... [0.008s] -Searching alignments... [0.318s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.204s] -Building query seed array... [0.091s] -Computing hash join... [0.087s] -Building seed filter... [0.008s] -Searching alignments... [0.234s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.226s] -Building query seed array... [0.095s] -Computing hash join... [0.088s] -Building seed filter... [0.008s] -Searching alignments... [0.205s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.231s] -Building query seed array... [0.101s] -Computing hash join... [0.088s] -Building seed filter... [0.008s] -Searching alignments... [0.219s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.2s] -Building query seed array... [0.09s] -Computing hash join... [0.088s] -Building seed filter... [0.007s] -Searching alignments... [0.203s] -Deallocating buffers... [0.052s] -Computing alignments... [2.586s] -Deallocating reference... [0.019s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.013s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.677s -Reported 27299 pairwise alignments, 27536 HSPs. -27299 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02/Sr_rh_Nn02_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn02_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Gspa.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Gspa.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.299s] -Masking queries... [0.104s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.046s] -Allocating buffers... [0s] -Loading reference sequences... [1.097s] -Masking reference... [0.693s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.327s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.235s] -Building query seed array... [0.037s] -Computing hash join... [0.079s] -Building seed filter... [0.005s] -Searching alignments... [0.061s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.247s] -Building query seed array... [0.037s] -Computing hash join... [0.065s] -Building seed filter... [0.004s] -Searching alignments... [0.06s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.255s] -Building query seed array... [0.042s] -Computing hash join... [0.063s] -Building seed filter... [0.005s] -Searching alignments... [0.06s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.208s] -Building query seed array... [0.037s] -Computing hash join... [0.062s] -Building seed filter... [0.004s] -Searching alignments... [0.057s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.202s] -Building query seed array... [0.035s] -Computing hash join... [0.06s] -Building seed filter... [0.004s] -Searching alignments... [0.054s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.235s] -Building query seed array... [0.04s] -Computing hash join... [0.057s] -Building seed filter... [0.004s] -Searching alignments... [0.052s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.247s] -Building query seed array... [0.041s] -Computing hash join... [0.061s] -Building seed filter... [0.004s] -Searching alignments... [0.051s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.203s] -Building query seed array... [0.036s] -Computing hash join... [0.06s] -Building seed filter... [0.004s] -Searching alignments... [0.052s] -Deallocating buffers... [0.055s] -Computing alignments... [0.628s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0.003s] -Deallocating queries... [0.003s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 6.484s -Reported 4770 pairwise alignments, 4832 HSPs. -4770 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa/BvE -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.299s] -Masking queries... [0.154s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.048s] -Allocating buffers... [0s] -Loading reference sequences... [0.99s] -Masking reference... [0.788s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.273s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.22s] -Building query seed array... [0.054s] -Computing hash join... [0.067s] -Building seed filter... [0.004s] -Searching alignments... [0.077s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.22s] -Building query seed array... [0.034s] -Computing hash join... [0.058s] -Building seed filter... [0.004s] -Searching alignments... [0.077s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.24s] -Building query seed array... [0.044s] -Computing hash join... [0.057s] -Building seed filter... [0.005s] -Searching alignments... [0.071s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.198s] -Building query seed array... [0.039s] -Computing hash join... [0.058s] -Building seed filter... [0.004s] -Searching alignments... [0.065s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.191s] -Building query seed array... [0.032s] -Computing hash join... [0.054s] -Building seed filter... [0.004s] -Searching alignments... [0.063s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.223s] -Building query seed array... [0.039s] -Computing hash join... [0.052s] -Building seed filter... [0.005s] -Searching alignments... [0.063s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.248s] -Building query seed array... [0.045s] -Computing hash join... [0.06s] -Building seed filter... [0.005s] -Searching alignments... [0.058s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.19s] -Building query seed array... [0.03s] -Computing hash join... [0.052s] -Building seed filter... [0.004s] -Searching alignments... [0.06s] -Deallocating buffers... [0.049s] -Computing alignments... [0.79s] -Deallocating reference... [0.016s] -Loading reference sequences... [0s] -Deallocating buffers... [0.003s] -Deallocating queries... [0.003s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 6.567s -Reported 9142 pairwise alignments, 9308 HSPs. -9142 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa/Sr_rh_Gspa_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Gspa_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn06.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn06.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.259s] -Masking queries... [0.362s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.129s] -Allocating buffers... [0s] -Loading reference sequences... [1.101s] -Masking reference... [0.69s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.299s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.23s] -Building query seed array... [0.104s] -Computing hash join... [0.111s] -Building seed filter... [0.007s] -Searching alignments... [0.145s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.255s] -Building query seed array... [0.1s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.144s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.253s] -Building query seed array... [0.103s] -Computing hash join... [0.1s] -Building seed filter... [0.006s] -Searching alignments... [0.141s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.214s] -Building query seed array... [0.092s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.141s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.212s] -Building query seed array... [0.099s] -Computing hash join... [0.098s] -Building seed filter... [0.008s] -Searching alignments... [0.13s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.244s] -Building query seed array... [0.109s] -Computing hash join... [0.101s] -Building seed filter... [0.008s] -Searching alignments... [0.127s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.247s] -Building query seed array... [0.106s] -Computing hash join... [0.097s] -Building seed filter... [0.008s] -Searching alignments... [0.137s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.212s] -Building query seed array... [0.102s] -Computing hash join... [0.1s] -Building seed filter... [0.009s] -Searching alignments... [0.13s] -Deallocating buffers... [0.058s] -Computing alignments... [1.366s] -Deallocating reference... [0.022s] -Loading reference sequences... [0s] -Deallocating buffers... [0.021s] -Deallocating queries... [0.017s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.048s -Reported 13937 pairwise alignments, 14011 HSPs. -13937 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.265s] -Masking queries... [0.333s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.133s] -Allocating buffers... [0s] -Loading reference sequences... [1.004s] -Masking reference... [0.644s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.272s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.22s] -Building query seed array... [0.107s] -Computing hash join... [0.129s] -Building seed filter... [0.007s] -Searching alignments... [0.357s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.231s] -Building query seed array... [0.099s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.323s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.234s] -Building query seed array... [0.103s] -Computing hash join... [0.093s] -Building seed filter... [0.008s] -Searching alignments... [0.218s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.195s] -Building query seed array... [0.087s] -Computing hash join... [0.094s] -Building seed filter... [0.008s] -Searching alignments... [0.312s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.198s] -Building query seed array... [0.089s] -Computing hash join... [0.092s] -Building seed filter... [0.008s] -Searching alignments... [0.251s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.227s] -Building query seed array... [0.099s] -Computing hash join... [0.092s] -Building seed filter... [0.009s] -Searching alignments... [0.235s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.238s] -Building query seed array... [0.107s] -Computing hash join... [0.093s] -Building seed filter... [0.008s] -Searching alignments... [0.234s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.192s] -Building query seed array... [0.091s] -Computing hash join... [0.091s] -Building seed filter... [0.008s] -Searching alignments... [0.226s] -Deallocating buffers... [0.051s] -Computing alignments... [2.637s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.018s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.998s -Reported 29695 pairwise alignments, 29910 HSPs. -29695 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06/Sr_rh_Nn06_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn06_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Bv02.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Bv02.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.833s] -Masking queries... [0.55s] -Building query seed set... [0.05s] -Algorithm: Double-indexed -Building query histograms... [0.161s] -Allocating buffers... [0s] -Loading reference sequences... [1.098s] -Masking reference... [0.696s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.298s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.233s] -Building query seed array... [0.127s] -Computing hash join... [0.113s] -Building seed filter... [0.006s] -Searching alignments... [0.182s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.241s] -Building query seed array... [0.11s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.18s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.245s] -Building query seed array... [0.13s] -Computing hash join... [0.101s] -Building seed filter... [0.007s] -Searching alignments... [0.173s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.209s] -Building query seed array... [0.097s] -Computing hash join... [0.095s] -Building seed filter... [0.007s] -Searching alignments... [0.174s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.211s] -Building query seed array... [0.101s] -Computing hash join... [0.097s] -Building seed filter... [0.007s] -Searching alignments... [0.154s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.238s] -Building query seed array... [0.114s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.158s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.25s] -Building query seed array... [0.115s] -Computing hash join... [0.1s] -Building seed filter... [0.007s] -Searching alignments... [0.162s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.216s] -Building query seed array... [0.1s] -Computing hash join... [0.095s] -Building seed filter... [0.006s] -Searching alignments... [0.157s] -Deallocating buffers... [0.058s] -Computing alignments... [1.721s] -Deallocating reference... [0.019s] -Loading reference sequences... [0s] -Deallocating buffers... [0.016s] -Deallocating queries... [0.022s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.493s -Reported 18788 pairwise alignments, 18972 HSPs. -18788 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.836s] -Masking queries... [0.465s] -Building query seed set... [0.049s] -Algorithm: Double-indexed -Building query histograms... [0.155s] -Allocating buffers... [0s] -Loading reference sequences... [0.978s] -Masking reference... [0.644s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.282s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.221s] -Building query seed array... [0.122s] -Computing hash join... [0.106s] -Building seed filter... [0.008s] -Searching alignments... [0.399s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.227s] -Building query seed array... [0.112s] -Computing hash join... [0.091s] -Building seed filter... [0.008s] -Searching alignments... [0.343s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.234s] -Building query seed array... [0.114s] -Computing hash join... [0.09s] -Building seed filter... [0.009s] -Searching alignments... [0.3s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.199s] -Building query seed array... [0.108s] -Computing hash join... [0.091s] -Building seed filter... [0.008s] -Searching alignments... [0.348s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.202s] -Building query seed array... [0.1s] -Computing hash join... [0.088s] -Building seed filter... [0.008s] -Searching alignments... [0.293s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.227s] -Building query seed array... [0.111s] -Computing hash join... [0.088s] -Building seed filter... [0.008s] -Searching alignments... [0.252s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.232s] -Building query seed array... [0.13s] -Computing hash join... [0.093s] -Building seed filter... [0.008s] -Searching alignments... [0.245s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.2s] -Building query seed array... [0.101s] -Computing hash join... [0.09s] -Building seed filter... [0.008s] -Searching alignments... [0.246s] -Deallocating buffers... [0.051s] -Computing alignments... [3.276s] -Deallocating reference... [0.022s] -Loading reference sequences... [0s] -Deallocating buffers... [0.017s] -Deallocating queries... [0.023s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.717s -Reported 38037 pairwise alignments, 38537 HSPs. -38037 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02/Sr_rh_Bv02_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Bv02_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Hind.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Hind.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.878s] -Masking queries... [0.263s] -Building query seed set... [0.04s] -Algorithm: Double-indexed -Building query histograms... [0.101s] -Allocating buffers... [0s] -Loading reference sequences... [1.102s] -Masking reference... [0.695s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.322s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.229s] -Building query seed array... [0.092s] -Computing hash join... [0.118s] -Building seed filter... [0.005s] -Searching alignments... [0.122s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.25s] -Building query seed array... [0.08s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.114s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.25s] -Building query seed array... [0.079s] -Computing hash join... [0.093s] -Building seed filter... [0.006s] -Searching alignments... [0.107s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.23s] -Building query seed array... [0.077s] -Computing hash join... [0.094s] -Building seed filter... [0.006s] -Searching alignments... [0.12s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.213s] -Building query seed array... [0.07s] -Computing hash join... [0.091s] -Building seed filter... [0.006s] -Searching alignments... [0.103s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.243s] -Building query seed array... [0.08s] -Computing hash join... [0.092s] -Building seed filter... [0.006s] -Searching alignments... [0.101s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.246s] -Building query seed array... [0.082s] -Computing hash join... [0.09s] -Building seed filter... [0.006s] -Searching alignments... [0.096s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.209s] -Building query seed array... [0.074s] -Computing hash join... [0.094s] -Building seed filter... [0.006s] -Searching alignments... [0.092s] -Deallocating buffers... [0.059s] -Computing alignments... [0.886s] -Deallocating reference... [0.028s] -Loading reference sequences... [0s] -Deallocating buffers... [0.011s] -Deallocating queries... [0.012s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 8.616s -Reported 7467 pairwise alignments, 7480 HSPs. -7467 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.888s] -Masking queries... [0.252s] -Building query seed set... [0.041s] -Algorithm: Double-indexed -Building query histograms... [0.114s] -Allocating buffers... [0s] -Loading reference sequences... [0.998s] -Masking reference... [0.663s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.286s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.221s] -Building query seed array... [0.085s] -Computing hash join... [0.118s] -Building seed filter... [0.006s] -Searching alignments... [0.139s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.226s] -Building query seed array... [0.082s] -Computing hash join... [0.09s] -Building seed filter... [0.005s] -Searching alignments... [0.144s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.079s] -Computing hash join... [0.087s] -Building seed filter... [0.006s] -Searching alignments... [0.13s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.195s] -Building query seed array... [0.069s] -Computing hash join... [0.086s] -Building seed filter... [0.005s] -Searching alignments... [0.131s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.194s] -Building query seed array... [0.074s] -Computing hash join... [0.085s] -Building seed filter... [0.005s] -Searching alignments... [0.115s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.222s] -Building query seed array... [0.078s] -Computing hash join... [0.084s] -Building seed filter... [0.005s] -Searching alignments... [0.127s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.227s] -Building query seed array... [0.081s] -Computing hash join... [0.089s] -Building seed filter... [0.007s] -Searching alignments... [0.118s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.191s] -Building query seed array... [0.073s] -Computing hash join... [0.087s] -Building seed filter... [0.007s] -Searching alignments... [0.111s] -Deallocating buffers... [0.05s] -Computing alignments... [1.503s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.012s] -Deallocating queries... [0.015s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.009s -Reported 14755 pairwise alignments, 14799 HSPs. -14755 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind/Sr_rh_Hind_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Hind_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn11.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn11.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.123s] -Masking queries... [0.301s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.127s] -Allocating buffers... [0s] -Loading reference sequences... [1.09s] -Masking reference... [0.688s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.286s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.231s] -Building query seed array... [0.102s] -Computing hash join... [0.12s] -Building seed filter... [0.007s] -Searching alignments... [0.134s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.245s] -Building query seed array... [0.098s] -Computing hash join... [0.096s] -Building seed filter... [0.008s] -Searching alignments... [0.132s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.255s] -Building query seed array... [0.093s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.122s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.212s] -Building query seed array... [0.082s] -Computing hash join... [0.096s] -Building seed filter... [0.008s] -Searching alignments... [0.125s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.208s] -Building query seed array... [0.084s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.112s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.236s] -Building query seed array... [0.091s] -Computing hash join... [0.097s] -Building seed filter... [0.006s] -Searching alignments... [0.114s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.243s] -Building query seed array... [0.086s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.111s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.212s] -Building query seed array... [0.082s] -Computing hash join... [0.101s] -Building seed filter... [0.007s] -Searching alignments... [0.111s] -Deallocating buffers... [0.056s] -Computing alignments... [1.084s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.014s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.263s -Reported 11697 pairwise alignments, 11771 HSPs. -11697 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.128s] -Masking queries... [0.307s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.119s] -Allocating buffers... [0s] -Loading reference sequences... [0.991s] -Masking reference... [0.636s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.269s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.216s] -Building query seed array... [0.098s] -Computing hash join... [0.109s] -Building seed filter... [0.006s] -Searching alignments... [0.295s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.229s] -Building query seed array... [0.088s] -Computing hash join... [0.088s] -Building seed filter... [0.007s] -Searching alignments... [0.181s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.243s] -Building query seed array... [0.09s] -Computing hash join... [0.088s] -Building seed filter... [0.008s] -Searching alignments... [0.17s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.197s] -Building query seed array... [0.075s] -Computing hash join... [0.091s] -Building seed filter... [0.006s] -Searching alignments... [0.166s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.194s] -Building query seed array... [0.086s] -Computing hash join... [0.093s] -Building seed filter... [0.007s] -Searching alignments... [0.152s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.221s] -Building query seed array... [0.087s] -Computing hash join... [0.091s] -Building seed filter... [0.007s] -Searching alignments... [0.163s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.095s] -Computing hash join... [0.093s] -Building seed filter... [0.007s] -Searching alignments... [0.155s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.193s] -Building query seed array... [0.085s] -Computing hash join... [0.091s] -Building seed filter... [0.007s] -Searching alignments... [0.151s] -Deallocating buffers... [0.051s] -Computing alignments... [1.964s] -Deallocating reference... [0.018s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.012s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.254s -Reported 25408 pairwise alignments, 25601 HSPs. -25408 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11/Sr_rh_Nn11_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn11_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Bv03.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Bv03.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.786s] -Masking queries... [0.459s] -Building query seed set... [0.05s] -Algorithm: Double-indexed -Building query histograms... [0.148s] -Allocating buffers... [0s] -Loading reference sequences... [1.108s] -Masking reference... [0.701s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.301s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.235s] -Building query seed array... [0.115s] -Computing hash join... [0.11s] -Building seed filter... [0.006s] -Searching alignments... [0.176s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.243s] -Building query seed array... [0.106s] -Computing hash join... [0.095s] -Building seed filter... [0.008s] -Searching alignments... [0.158s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.246s] -Building query seed array... [0.107s] -Computing hash join... [0.097s] -Building seed filter... [0.008s] -Searching alignments... [0.17s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.215s] -Building query seed array... [0.097s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.161s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.211s] -Building query seed array... [0.094s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.151s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.24s] -Building query seed array... [0.106s] -Computing hash join... [0.093s] -Building seed filter... [0.006s] -Searching alignments... [0.15s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.244s] -Building query seed array... [0.113s] -Computing hash join... [0.094s] -Building seed filter... [0.006s] -Searching alignments... [0.153s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.205s] -Building query seed array... [0.091s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.149s] -Deallocating buffers... [0.056s] -Computing alignments... [1.651s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.02s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.134s -Reported 18214 pairwise alignments, 18404 HSPs. -18214 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03/BvE -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.797s] -Masking queries... [0.454s] -Building query seed set... [0.051s] -Algorithm: Double-indexed -Building query histograms... [0.149s] -Allocating buffers... [0s] -Loading reference sequences... [1.046s] -Masking reference... [0.659s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.279s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.227s] -Building query seed array... [0.107s] -Computing hash join... [0.108s] -Building seed filter... [0.009s] -Searching alignments... [0.363s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.228s] -Building query seed array... [0.108s] -Computing hash join... [0.088s] -Building seed filter... [0.007s] -Searching alignments... [0.313s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.232s] -Building query seed array... [0.107s] -Computing hash join... [0.09s] -Building seed filter... [0.006s] -Searching alignments... [0.297s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.197s] -Building query seed array... [0.098s] -Computing hash join... [0.091s] -Building seed filter... [0.006s] -Searching alignments... [0.347s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.202s] -Building query seed array... [0.105s] -Computing hash join... [0.087s] -Building seed filter... [0.007s] -Searching alignments... [0.255s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.224s] -Building query seed array... [0.106s] -Computing hash join... [0.09s] -Building seed filter... [0.008s] -Searching alignments... [0.253s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.234s] -Building query seed array... [0.107s] -Computing hash join... [0.088s] -Building seed filter... [0.009s] -Searching alignments... [0.229s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.196s] -Building query seed array... [0.098s] -Computing hash join... [0.088s] -Building seed filter... [0.007s] -Searching alignments... [0.233s] -Deallocating buffers... [0.05s] -Computing alignments... [3.164s] -Deallocating reference... [0.025s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.022s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.417s -Reported 36335 pairwise alignments, 36838 HSPs. -36335 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03/Sr_rh_Bv03_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Bv03_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Gsp1.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Gsp1.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.606s] -Masking queries... [0.179s] -Building query seed set... [0.042s] -Algorithm: Double-indexed -Building query histograms... [0.071s] -Allocating buffers... [0s] -Loading reference sequences... [1.127s] -Masking reference... [0.691s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.311s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.24s] -Building query seed array... [0.068s] -Computing hash join... [0.118s] -Building seed filter... [0.005s] -Searching alignments... [0.092s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.239s] -Building query seed array... [0.059s] -Computing hash join... [0.088s] -Building seed filter... [0.005s] -Searching alignments... [0.084s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.253s] -Building query seed array... [0.055s] -Computing hash join... [0.088s] -Building seed filter... [0.005s] -Searching alignments... [0.08s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.212s] -Building query seed array... [0.053s] -Computing hash join... [0.082s] -Building seed filter... [0.006s] -Searching alignments... [0.081s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.211s] -Building query seed array... [0.054s] -Computing hash join... [0.083s] -Building seed filter... [0.005s] -Searching alignments... [0.074s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.233s] -Building query seed array... [0.057s] -Computing hash join... [0.082s] -Building seed filter... [0.006s] -Searching alignments... [0.078s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.246s] -Building query seed array... [0.059s] -Computing hash join... [0.081s] -Building seed filter... [0.006s] -Searching alignments... [0.073s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.203s] -Building query seed array... [0.053s] -Computing hash join... [0.086s] -Building seed filter... [0.006s] -Searching alignments... [0.073s] -Deallocating buffers... [0.057s] -Computing alignments... [0.674s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0.006s] -Deallocating queries... [0.007s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 7.525s -Reported 6372 pairwise alignments, 6381 HSPs. -6372 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.615s] -Masking queries... [0.175s] -Building query seed set... [0.041s] -Algorithm: Double-indexed -Building query histograms... [0.067s] -Allocating buffers... [0s] -Loading reference sequences... [1.021s] -Masking reference... [0.638s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.27s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.216s] -Building query seed array... [0.067s] -Computing hash join... [0.111s] -Building seed filter... [0.005s] -Searching alignments... [0.112s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.22s] -Building query seed array... [0.059s] -Computing hash join... [0.084s] -Building seed filter... [0.006s] -Searching alignments... [0.124s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.249s] -Building query seed array... [0.069s] -Computing hash join... [0.088s] -Building seed filter... [0.006s] -Searching alignments... [0.109s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.194s] -Building query seed array... [0.054s] -Computing hash join... [0.084s] -Building seed filter... [0.005s] -Searching alignments... [0.111s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.196s] -Building query seed array... [0.052s] -Computing hash join... [0.074s] -Building seed filter... [0.006s] -Searching alignments... [0.093s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.221s] -Building query seed array... [0.054s] -Computing hash join... [0.078s] -Building seed filter... [0.006s] -Searching alignments... [0.098s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.228s] -Building query seed array... [0.053s] -Computing hash join... [0.077s] -Building seed filter... [0.006s] -Searching alignments... [0.091s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.19s] -Building query seed array... [0.052s] -Computing hash join... [0.079s] -Building seed filter... [0.006s] -Searching alignments... [0.096s] -Deallocating buffers... [0.049s] -Computing alignments... [1.173s] -Deallocating reference... [0.017s] -Loading reference sequences... [0s] -Deallocating buffers... [0.008s] -Deallocating queries... [0.009s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 7.856s -Reported 13026 pairwise alignments, 13050 HSPs. -13026 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1/Sr_rh_Gsp1_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Gsp1_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Bv06.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Bv06.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.977s] -Masking queries... [0.29s] -Building query seed set... [0.051s] -Algorithm: Double-indexed -Building query histograms... [0.086s] -Allocating buffers... [0s] -Loading reference sequences... [1.09s] -Masking reference... [0.691s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.318s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.229s] -Building query seed array... [0.072s] -Computing hash join... [0.134s] -Building seed filter... [0.006s] -Searching alignments... [0.112s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.242s] -Building query seed array... [0.063s] -Computing hash join... [0.097s] -Building seed filter... [0.006s] -Searching alignments... [0.105s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.254s] -Building query seed array... [0.067s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.099s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.221s] -Building query seed array... [0.067s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.097s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.213s] -Building query seed array... [0.059s] -Computing hash join... [0.089s] -Building seed filter... [0.006s] -Searching alignments... [0.089s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.251s] -Building query seed array... [0.066s] -Computing hash join... [0.09s] -Building seed filter... [0.005s] -Searching alignments... [0.085s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.243s] -Building query seed array... [0.072s] -Computing hash join... [0.091s] -Building seed filter... [0.006s] -Searching alignments... [0.095s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.206s] -Building query seed array... [0.061s] -Computing hash join... [0.089s] -Building seed filter... [0.006s] -Searching alignments... [0.089s] -Deallocating buffers... [0.059s] -Computing alignments... [0.916s] -Deallocating reference... [0.023s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.009s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 8.558s -Reported 11454 pairwise alignments, 11535 HSPs. -11454 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0.001s] -Opening the output file... [0s] -Loading query sequences... [0.99s] -Masking queries... [0.258s] -Building query seed set... [0.048s] -Algorithm: Double-indexed -Building query histograms... [0.088s] -Allocating buffers... [0s] -Loading reference sequences... [0.994s] -Masking reference... [0.645s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.273s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.211s] -Building query seed array... [0.071s] -Computing hash join... [0.117s] -Building seed filter... [0.006s] -Searching alignments... [0.162s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.226s] -Building query seed array... [0.065s] -Computing hash join... [0.093s] -Building seed filter... [0.005s] -Searching alignments... [0.171s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.231s] -Building query seed array... [0.069s] -Computing hash join... [0.093s] -Building seed filter... [0.006s] -Searching alignments... [0.148s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.198s] -Building query seed array... [0.062s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.179s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.201s] -Building query seed array... [0.06s] -Computing hash join... [0.089s] -Building seed filter... [0.006s] -Searching alignments... [0.136s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.229s] -Building query seed array... [0.068s] -Computing hash join... [0.084s] -Building seed filter... [0.005s] -Searching alignments... [0.139s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.244s] -Building query seed array... [0.073s] -Computing hash join... [0.09s] -Building seed filter... [0.006s] -Searching alignments... [0.139s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.192s] -Building query seed array... [0.054s] -Computing hash join... [0.088s] -Building seed filter... [0.006s] -Searching alignments... [0.13s] -Deallocating buffers... [0.05s] -Computing alignments... [1.598s] -Deallocating reference... [0.018s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.012s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.277s -Reported 22234 pairwise alignments, 22429 HSPs. -22234 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06/Sr_rh_Bv06_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Bv06_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Gl01.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Gl01.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.043s] -Masking queries... [0.023s] -Building query seed set... [0.029s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [1.086s] -Masking reference... [0.71s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.304s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.243s] -Building query seed array... [0.012s] -Computing hash join... [0.076s] -Building seed filter... [0.004s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.238s] -Building query seed array... [0.011s] -Computing hash join... [0.063s] -Building seed filter... [0.004s] -Searching alignments... [0.01s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.245s] -Building query seed array... [0.01s] -Computing hash join... [0.055s] -Building seed filter... [0.004s] -Searching alignments... [0.009s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.205s] -Building query seed array... [0.006s] -Computing hash join... [0.051s] -Building seed filter... [0.004s] -Searching alignments... [0.01s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.208s] -Building query seed array... [0.009s] -Computing hash join... [0.057s] -Building seed filter... [0.004s] -Searching alignments... [0.009s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.234s] -Building query seed array... [0.007s] -Computing hash join... [0.055s] -Building seed filter... [0.004s] -Searching alignments... [0.01s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.248s] -Building query seed array... [0.011s] -Computing hash join... [0.054s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.206s] -Building query seed array... [0.007s] -Computing hash join... [0.057s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Deallocating buffers... [0.057s] -Computing alignments... [0.126s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 4.935s -Reported 901 pairwise alignments, 903 HSPs. -901 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.034s] -Masking queries... [0.026s] -Building query seed set... [0.029s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [1.012s] -Masking reference... [0.627s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.288s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.229s] -Building query seed array... [0.023s] -Computing hash join... [0.053s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.231s] -Building query seed array... [0.018s] -Computing hash join... [0.049s] -Building seed filter... [0.004s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.236s] -Building query seed array... [0.015s] -Computing hash join... [0.048s] -Building seed filter... [0.004s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.202s] -Building query seed array... [0.015s] -Computing hash join... [0.053s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.2s] -Building query seed array... [0.018s] -Computing hash join... [0.05s] -Building seed filter... [0.004s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.22s] -Building query seed array... [0.016s] -Computing hash join... [0.049s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.228s] -Building query seed array... [0.015s] -Computing hash join... [0.05s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.2s] -Building query seed array... [0.018s] -Computing hash join... [0.049s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Deallocating buffers... [0.052s] -Computing alignments... [0.168s] -Deallocating reference... [0.02s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 4.846s -Reported 2013 pairwise alignments, 2017 HSPs. -2013 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01/Sr_rh_Gl01_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Gl01_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Esca.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Esca.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.72s] -Masking queries... [0.231s] -Building query seed set... [0.042s] -Algorithm: Double-indexed -Building query histograms... [0.074s] -Allocating buffers... [0s] -Loading reference sequences... [1.084s] -Masking reference... [0.687s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.303s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.227s] -Building query seed array... [0.07s] -Computing hash join... [0.127s] -Building seed filter... [0.006s] -Searching alignments... [0.092s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.24s] -Building query seed array... [0.057s] -Computing hash join... [0.088s] -Building seed filter... [0.005s] -Searching alignments... [0.087s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.249s] -Building query seed array... [0.054s] -Computing hash join... [0.081s] -Building seed filter... [0.005s] -Searching alignments... [0.082s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.213s] -Building query seed array... [0.053s] -Computing hash join... [0.08s] -Building seed filter... [0.005s] -Searching alignments... [0.086s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.209s] -Building query seed array... [0.053s] -Computing hash join... [0.077s] -Building seed filter... [0.004s] -Searching alignments... [0.073s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.235s] -Building query seed array... [0.053s] -Computing hash join... [0.074s] -Building seed filter... [0.005s] -Searching alignments... [0.077s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.262s] -Building query seed array... [0.07s] -Computing hash join... [0.08s] -Building seed filter... [0.005s] -Searching alignments... [0.075s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.213s] -Building query seed array... [0.055s] -Computing hash join... [0.074s] -Building seed filter... [0.005s] -Searching alignments... [0.073s] -Deallocating buffers... [0.057s] -Computing alignments... [0.777s] -Deallocating reference... [0.025s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.008s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 7.742s -Reported 8279 pairwise alignments, 8300 HSPs. -8279 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.723s] -Masking queries... [0.215s] -Building query seed set... [0.043s] -Algorithm: Double-indexed -Building query histograms... [0.082s] -Allocating buffers... [0s] -Loading reference sequences... [1.018s] -Masking reference... [0.642s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.296s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.218s] -Building query seed array... [0.064s] -Computing hash join... [0.102s] -Building seed filter... [0.006s] -Searching alignments... [0.162s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.222s] -Building query seed array... [0.056s] -Computing hash join... [0.08s] -Building seed filter... [0.005s] -Searching alignments... [0.137s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.231s] -Building query seed array... [0.054s] -Computing hash join... [0.076s] -Building seed filter... [0.005s] -Searching alignments... [0.121s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.197s] -Building query seed array... [0.054s] -Computing hash join... [0.076s] -Building seed filter... [0.005s] -Searching alignments... [0.136s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.194s] -Building query seed array... [0.056s] -Computing hash join... [0.078s] -Building seed filter... [0.006s] -Searching alignments... [0.125s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.226s] -Building query seed array... [0.066s] -Computing hash join... [0.08s] -Building seed filter... [0.005s] -Searching alignments... [0.108s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.232s] -Building query seed array... [0.056s] -Computing hash join... [0.075s] -Building seed filter... [0.006s] -Searching alignments... [0.11s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.195s] -Building query seed array... [0.048s] -Computing hash join... [0.086s] -Building seed filter... [0.005s] -Searching alignments... [0.116s] -Deallocating buffers... [0.049s] -Computing alignments... [1.318s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.01s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 8.354s -Reported 17266 pairwise alignments, 17309 HSPs. -17266 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca/Sr_rh_Esca_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Esca_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Calb.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Calb.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.792s] -Masking queries... [0.208s] -Building query seed set... [0.041s] -Algorithm: Double-indexed -Building query histograms... [0.082s] -Allocating buffers... [0s] -Loading reference sequences... [1.109s] -Masking reference... [0.705s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.306s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.233s] -Building query seed array... [0.076s] -Computing hash join... [0.131s] -Building seed filter... [0.004s] -Searching alignments... [0.104s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.249s] -Building query seed array... [0.064s] -Computing hash join... [0.107s] -Building seed filter... [0.006s] -Searching alignments... [0.099s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.249s] -Building query seed array... [0.063s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.093s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.207s] -Building query seed array... [0.062s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.089s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.208s] -Building query seed array... [0.061s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.083s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.236s] -Building query seed array... [0.063s] -Computing hash join... [0.094s] -Building seed filter... [0.006s] -Searching alignments... [0.083s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.242s] -Building query seed array... [0.066s] -Computing hash join... [0.095s] -Building seed filter... [0.006s] -Searching alignments... [0.082s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.215s] -Building query seed array... [0.065s] -Computing hash join... [0.094s] -Building seed filter... [0.006s] -Searching alignments... [0.081s] -Deallocating buffers... [0.056s] -Computing alignments... [0.797s] -Deallocating reference... [0.023s] -Loading reference sequences... [0s] -Deallocating buffers... [0.01s] -Deallocating queries... [0.007s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 8.114s -Reported 7719 pairwise alignments, 7754 HSPs. -7719 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.79s] -Masking queries... [0.213s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.086s] -Allocating buffers... [0s] -Loading reference sequences... [1.004s] -Masking reference... [0.641s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.265s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.216s] -Building query seed array... [0.079s] -Computing hash join... [0.118s] -Building seed filter... [0.005s] -Searching alignments... [0.142s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.226s] -Building query seed array... [0.066s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.137s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.229s] -Building query seed array... [0.062s] -Computing hash join... [0.092s] -Building seed filter... [0.007s] -Searching alignments... [0.12s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.195s] -Building query seed array... [0.055s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.133s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.196s] -Building query seed array... [0.055s] -Computing hash join... [0.091s] -Building seed filter... [0.005s] -Searching alignments... [0.118s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.223s] -Building query seed array... [0.061s] -Computing hash join... [0.089s] -Building seed filter... [0.005s] -Searching alignments... [0.122s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.228s] -Building query seed array... [0.062s] -Computing hash join... [0.09s] -Building seed filter... [0.005s] -Searching alignments... [0.114s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.191s] -Building query seed array... [0.063s] -Computing hash join... [0.089s] -Building seed filter... [0.006s] -Searching alignments... [0.112s] -Deallocating buffers... [0.05s] -Computing alignments... [1.391s] -Deallocating reference... [0.02s] -Loading reference sequences... [0s] -Deallocating buffers... [0.01s] -Deallocating queries... [0.01s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 8.576s -Reported 15220 pairwise alignments, 15279 HSPs. -15220 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb/Sr_rh_Calb_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Calb_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Emac.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Emac.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.739s] -Masking queries... [0.202s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.086s] -Allocating buffers... [0s] -Loading reference sequences... [1.109s] -Masking reference... [0.69s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.306s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.239s] -Building query seed array... [0.076s] -Computing hash join... [0.133s] -Building seed filter... [0.006s] -Searching alignments... [0.096s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.241s] -Building query seed array... [0.068s] -Computing hash join... [0.109s] -Building seed filter... [0.005s] -Searching alignments... [0.097s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.257s] -Building query seed array... [0.076s] -Computing hash join... [0.105s] -Building seed filter... [0.006s] -Searching alignments... [0.095s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.063s] -Computing hash join... [0.1s] -Building seed filter... [0.006s] -Searching alignments... [0.095s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.208s] -Building query seed array... [0.06s] -Computing hash join... [0.1s] -Building seed filter... [0.006s] -Searching alignments... [0.088s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.243s] -Building query seed array... [0.074s] -Computing hash join... [0.103s] -Building seed filter... [0.005s] -Searching alignments... [0.087s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.243s] -Building query seed array... [0.068s] -Computing hash join... [0.1s] -Building seed filter... [0.005s] -Searching alignments... [0.086s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.207s] -Building query seed array... [0.063s] -Computing hash join... [0.1s] -Building seed filter... [0.005s] -Searching alignments... [0.083s] -Deallocating buffers... [0.056s] -Computing alignments... [0.768s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0.009s] -Deallocating queries... [0.007s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 8.096s -Reported 6356 pairwise alignments, 6370 HSPs. -6356 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.751s] -Masking queries... [0.21s] -Building query seed set... [0.042s] -Algorithm: Double-indexed -Building query histograms... [0.091s] -Allocating buffers... [0s] -Loading reference sequences... [0.978s] -Masking reference... [0.64s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.277s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.225s] -Building query seed array... [0.08s] -Computing hash join... [0.145s] -Building seed filter... [0.005s] -Searching alignments... [0.115s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.22s] -Building query seed array... [0.065s] -Computing hash join... [0.101s] -Building seed filter... [0.006s] -Searching alignments... [0.112s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.234s] -Building query seed array... [0.074s] -Computing hash join... [0.101s] -Building seed filter... [0.006s] -Searching alignments... [0.111s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.196s] -Building query seed array... [0.064s] -Computing hash join... [0.098s] -Building seed filter... [0.005s] -Searching alignments... [0.11s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.194s] -Building query seed array... [0.06s] -Computing hash join... [0.096s] -Building seed filter... [0.005s] -Searching alignments... [0.099s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.217s] -Building query seed array... [0.072s] -Computing hash join... [0.097s] -Building seed filter... [0.005s] -Searching alignments... [0.097s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.229s] -Building query seed array... [0.073s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.096s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.189s] -Building query seed array... [0.062s] -Computing hash join... [0.099s] -Building seed filter... [0.005s] -Searching alignments... [0.099s] -Deallocating buffers... [0.05s] -Computing alignments... [1.187s] -Deallocating reference... [0.018s] -Loading reference sequences... [0s] -Deallocating buffers... [0.011s] -Deallocating queries... [0.009s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 8.282s -Reported 12686 pairwise alignments, 12732 HSPs. -12686 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac/Sr_rh_Emac_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Emac_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn05.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn05.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.137s] -Masking queries... [0.299s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.121s] -Allocating buffers... [0s] -Loading reference sequences... [1.113s] -Masking reference... [0.703s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.297s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.233s] -Building query seed array... [0.092s] -Computing hash join... [0.113s] -Building seed filter... [0.008s] -Searching alignments... [0.13s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.243s] -Building query seed array... [0.089s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.124s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.249s] -Building query seed array... [0.087s] -Computing hash join... [0.094s] -Building seed filter... [0.006s] -Searching alignments... [0.121s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.211s] -Building query seed array... [0.082s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.126s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.211s] -Building query seed array... [0.08s] -Computing hash join... [0.095s] -Building seed filter... [0.006s] -Searching alignments... [0.115s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.241s] -Building query seed array... [0.088s] -Computing hash join... [0.093s] -Building seed filter... [0.008s] -Searching alignments... [0.115s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.248s] -Building query seed array... [0.091s] -Computing hash join... [0.097s] -Building seed filter... [0.009s] -Searching alignments... [0.114s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.081s] -Computing hash join... [0.099s] -Building seed filter... [0.008s] -Searching alignments... [0.117s] -Deallocating buffers... [0.058s] -Computing alignments... [1.143s] -Deallocating reference... [0.019s] -Loading reference sequences... [0s] -Deallocating buffers... [0.02s] -Deallocating queries... [0.013s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.346s -Reported 11705 pairwise alignments, 11759 HSPs. -11705 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05/BvE -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.144s] -Masking queries... [0.297s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.129s] -Allocating buffers... [0s] -Loading reference sequences... [0.997s] -Masking reference... [0.638s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.27s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.221s] -Building query seed array... [0.108s] -Computing hash join... [0.142s] -Building seed filter... [0.005s] -Searching alignments... [0.321s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.229s] -Building query seed array... [0.086s] -Computing hash join... [0.092s] -Building seed filter... [0.007s] -Searching alignments... [0.265s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.09s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.264s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.203s] -Building query seed array... [0.076s] -Computing hash join... [0.092s] -Building seed filter... [0.007s] -Searching alignments... [0.274s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.197s] -Building query seed array... [0.075s] -Computing hash join... [0.089s] -Building seed filter... [0.007s] -Searching alignments... [0.17s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.231s] -Building query seed array... [0.093s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.22s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.229s] -Building query seed array... [0.095s] -Computing hash join... [0.091s] -Building seed filter... [0.007s] -Searching alignments... [0.203s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.198s] -Building query seed array... [0.079s] -Computing hash join... [0.092s] -Building seed filter... [0.006s] -Searching alignments... [0.157s] -Deallocating buffers... [0.051s] -Computing alignments... [2.168s] -Deallocating reference... [0.017s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.011s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.967s -Reported 25364 pairwise alignments, 25538 HSPs. -25364 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05/Sr_rh_Nn05_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn05_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn10.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn10.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.355s] -Masking queries... [0.376s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.145s] -Allocating buffers... [0s] -Loading reference sequences... [1.106s] -Masking reference... [0.694s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.297s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.237s] -Building query seed array... [0.115s] -Computing hash join... [0.109s] -Building seed filter... [0.006s] -Searching alignments... [0.16s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.244s] -Building query seed array... [0.106s] -Computing hash join... [0.098s] -Building seed filter... [0.008s] -Searching alignments... [0.158s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.256s] -Building query seed array... [0.11s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.161s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.212s] -Building query seed array... [0.104s] -Computing hash join... [0.104s] -Building seed filter... [0.007s] -Searching alignments... [0.151s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.209s] -Building query seed array... [0.1s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.14s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.245s] -Building query seed array... [0.11s] -Computing hash join... [0.097s] -Building seed filter... [0.007s] -Searching alignments... [0.14s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.251s] -Building query seed array... [0.11s] -Computing hash join... [0.102s] -Building seed filter... [0.007s] -Searching alignments... [0.14s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.211s] -Building query seed array... [0.1s] -Computing hash join... [0.099s] -Building seed filter... [0.007s] -Searching alignments... [0.139s] -Deallocating buffers... [0.058s] -Computing alignments... [1.734s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0.016s] -Deallocating queries... [0.015s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.675s -Reported 14496 pairwise alignments, 14578 HSPs. -14496 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.363s] -Masking queries... [0.364s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.16s] -Allocating buffers... [0s] -Loading reference sequences... [0.984s] -Masking reference... [0.648s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.276s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.212s] -Building query seed array... [0.114s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.433s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.224s] -Building query seed array... [0.112s] -Computing hash join... [0.091s] -Building seed filter... [0.007s] -Searching alignments... [0.341s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.114s] -Computing hash join... [0.092s] -Building seed filter... [0.007s] -Searching alignments... [0.309s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.199s] -Building query seed array... [0.098s] -Computing hash join... [0.093s] -Building seed filter... [0.007s] -Searching alignments... [0.362s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.196s] -Building query seed array... [0.096s] -Computing hash join... [0.088s] -Building seed filter... [0.007s] -Searching alignments... [0.278s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.222s] -Building query seed array... [0.107s] -Computing hash join... [0.091s] -Building seed filter... [0.007s] -Searching alignments... [0.262s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.23s] -Building query seed array... [0.115s] -Computing hash join... [0.089s] -Building seed filter... [0.007s] -Searching alignments... [0.247s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.198s] -Building query seed array... [0.104s] -Computing hash join... [0.092s] -Building seed filter... [0.007s] -Searching alignments... [0.254s] -Deallocating buffers... [0.05s] -Computing alignments... [3.031s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.018s] -Deallocating queries... [0.019s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 12.87s -Reported 29484 pairwise alignments, 29722 HSPs. -29484 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10/Sr_rh_Nn10_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn10_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn03.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn03.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.196s] -Masking queries... [0.334s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.124s] -Allocating buffers... [0s] -Loading reference sequences... [1.09s] -Masking reference... [0.688s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.293s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.231s] -Building query seed array... [0.096s] -Computing hash join... [0.107s] -Building seed filter... [0.008s] -Searching alignments... [0.133s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.24s] -Building query seed array... [0.091s] -Computing hash join... [0.093s] -Building seed filter... [0.006s] -Searching alignments... [0.133s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.25s] -Building query seed array... [0.099s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.134s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.213s] -Building query seed array... [0.083s] -Computing hash join... [0.092s] -Building seed filter... [0.006s] -Searching alignments... [0.134s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.211s] -Building query seed array... [0.08s] -Computing hash join... [0.094s] -Building seed filter... [0.006s] -Searching alignments... [0.117s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.238s] -Building query seed array... [0.092s] -Computing hash join... [0.093s] -Building seed filter... [0.006s] -Searching alignments... [0.121s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.251s] -Building query seed array... [0.094s] -Computing hash join... [0.094s] -Building seed filter... [0.005s] -Searching alignments... [0.122s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.211s] -Building query seed array... [0.088s] -Computing hash join... [0.094s] -Building seed filter... [0.006s] -Searching alignments... [0.119s] -Deallocating buffers... [0.058s] -Computing alignments... [1.366s] -Deallocating reference... [0.022s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.013s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.678s -Reported 12756 pairwise alignments, 12883 HSPs. -12756 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.195s] -Masking queries... [0.316s] -Building query seed set... [0.04s] -Algorithm: Double-indexed -Building query histograms... [0.127s] -Allocating buffers... [0s] -Loading reference sequences... [1.001s] -Masking reference... [0.637s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.267s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.218s] -Building query seed array... [0.107s] -Computing hash join... [0.104s] -Building seed filter... [0.012s] -Searching alignments... [0.298s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.246s] -Building query seed array... [0.1s] -Computing hash join... [0.094s] -Building seed filter... [0.008s] -Searching alignments... [0.261s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.246s] -Building query seed array... [0.107s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.231s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.197s] -Building query seed array... [0.089s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.267s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.195s] -Building query seed array... [0.082s] -Computing hash join... [0.087s] -Building seed filter... [0.008s] -Searching alignments... [0.213s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.221s] -Building query seed array... [0.092s] -Computing hash join... [0.09s] -Building seed filter... [0.008s] -Searching alignments... [0.188s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.232s] -Building query seed array... [0.101s] -Computing hash join... [0.09s] -Building seed filter... [0.008s] -Searching alignments... [0.184s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.201s] -Building query seed array... [0.084s] -Computing hash join... [0.086s] -Building seed filter... [0.008s] -Searching alignments... [0.19s] -Deallocating buffers... [0.052s] -Computing alignments... [2.409s] -Deallocating reference... [0.022s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.017s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.289s -Reported 26522 pairwise alignments, 26813 HSPs. -26522 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03/Sr_rh_Nn03_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn03_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Halb.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Halb.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.186s] -Masking queries... [0.342s] -Building query seed set... [0.066s] -Algorithm: Double-indexed -Building query histograms... [0.137s] -Allocating buffers... [0s] -Loading reference sequences... [1.119s] -Masking reference... [0.698s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.297s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.228s] -Building query seed array... [0.103s] -Computing hash join... [0.109s] -Building seed filter... [0.006s] -Searching alignments... [0.181s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.255s] -Building query seed array... [0.11s] -Computing hash join... [0.095s] -Building seed filter... [0.006s] -Searching alignments... [0.164s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.257s] -Building query seed array... [0.112s] -Computing hash join... [0.095s] -Building seed filter... [0.007s] -Searching alignments... [0.157s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.213s] -Building query seed array... [0.096s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.159s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.213s] -Building query seed array... [0.089s] -Computing hash join... [0.089s] -Building seed filter... [0.006s] -Searching alignments... [0.147s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.243s] -Building query seed array... [0.106s] -Computing hash join... [0.092s] -Building seed filter... [0.005s] -Searching alignments... [0.14s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.249s] -Building query seed array... [0.107s] -Computing hash join... [0.093s] -Building seed filter... [0.006s] -Searching alignments... [0.146s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.211s] -Building query seed array... [0.09s] -Computing hash join... [0.089s] -Building seed filter... [0.006s] -Searching alignments... [0.146s] -Deallocating buffers... [0.057s] -Computing alignments... [1.406s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.019s] -Deallocating queries... [0.016s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.139s -Reported 9580 pairwise alignments, 9606 HSPs. -9580 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.18s] -Masking queries... [0.34s] -Building query seed set... [0.068s] -Algorithm: Double-indexed -Building query histograms... [0.138s] -Allocating buffers... [0s] -Loading reference sequences... [0.984s] -Masking reference... [0.639s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.28s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.219s] -Building query seed array... [0.103s] -Computing hash join... [0.112s] -Building seed filter... [0.007s] -Searching alignments... [0.19s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.225s] -Building query seed array... [0.112s] -Computing hash join... [0.088s] -Building seed filter... [0.005s] -Searching alignments... [0.185s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.234s] -Building query seed array... [0.106s] -Computing hash join... [0.089s] -Building seed filter... [0.005s] -Searching alignments... [0.176s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.199s] -Building query seed array... [0.096s] -Computing hash join... [0.087s] -Building seed filter... [0.005s] -Searching alignments... [0.197s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.2s] -Building query seed array... [0.092s] -Computing hash join... [0.085s] -Building seed filter... [0.005s] -Searching alignments... [0.165s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.225s] -Building query seed array... [0.106s] -Computing hash join... [0.086s] -Building seed filter... [0.006s] -Searching alignments... [0.163s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.23s] -Building query seed array... [0.101s] -Computing hash join... [0.084s] -Building seed filter... [0.006s] -Searching alignments... [0.155s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.195s] -Building query seed array... [0.092s] -Computing hash join... [0.084s] -Building seed filter... [0.01s] -Searching alignments... [0.147s] -Deallocating buffers... [0.05s] -Computing alignments... [2.243s] -Deallocating reference... [0.018s] -Loading reference sequences... [0s] -Deallocating buffers... [0.018s] -Deallocating queries... [0.014s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.696s -Reported 20722 pairwise alignments, 20823 HSPs. -20722 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb/Sr_rh_Halb_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Halb_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn08.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn08.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.103s] -Masking queries... [0.349s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.109s] -Allocating buffers... [0s] -Loading reference sequences... [1.095s] -Masking reference... [0.693s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.288s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.23s] -Building query seed array... [0.091s] -Computing hash join... [0.117s] -Building seed filter... [0.006s] -Searching alignments... [0.12s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.245s] -Building query seed array... [0.083s] -Computing hash join... [0.097s] -Building seed filter... [0.005s] -Searching alignments... [0.108s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.253s] -Building query seed array... [0.084s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.113s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.209s] -Building query seed array... [0.069s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.112s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.21s] -Building query seed array... [0.074s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.099s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.241s] -Building query seed array... [0.084s] -Computing hash join... [0.095s] -Building seed filter... [0.006s] -Searching alignments... [0.095s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.245s] -Building query seed array... [0.082s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.103s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.075s] -Computing hash join... [0.096s] -Building seed filter... [0.005s] -Searching alignments... [0.096s] -Deallocating buffers... [0.057s] -Computing alignments... [1.258s] -Deallocating reference... [0.02s] -Loading reference sequences... [0s] -Deallocating buffers... [0.011s] -Deallocating queries... [0.012s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.25s -Reported 12050 pairwise alignments, 12165 HSPs. -12050 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.099s] -Masking queries... [0.286s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.126s] -Allocating buffers... [0s] -Loading reference sequences... [0.98s] -Masking reference... [0.639s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.282s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.221s] -Building query seed array... [0.095s] -Computing hash join... [0.115s] -Building seed filter... [0.006s] -Searching alignments... [0.385s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.224s] -Building query seed array... [0.078s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.293s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.231s] -Building query seed array... [0.087s] -Computing hash join... [0.091s] -Building seed filter... [0.006s] -Searching alignments... [0.273s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.201s] -Building query seed array... [0.07s] -Computing hash join... [0.091s] -Building seed filter... [0.006s] -Searching alignments... [0.262s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.199s] -Building query seed array... [0.073s] -Computing hash join... [0.094s] -Building seed filter... [0.006s] -Searching alignments... [0.237s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.225s] -Building query seed array... [0.085s] -Computing hash join... [0.086s] -Building seed filter... [0.006s] -Searching alignments... [0.204s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.239s] -Building query seed array... [0.086s] -Computing hash join... [0.089s] -Building seed filter... [0.005s] -Searching alignments... [0.221s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.198s] -Building query seed array... [0.072s] -Computing hash join... [0.088s] -Building seed filter... [0.006s] -Searching alignments... [0.249s] -Deallocating buffers... [0.052s] -Computing alignments... [2.283s] -Deallocating reference... [0.018s] -Loading reference sequences... [0s] -Deallocating buffers... [0.012s] -Deallocating queries... [0.017s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.188s -Reported 24842 pairwise alignments, 25154 HSPs. -24842 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08/Sr_rh_Nn08_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn08_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Tx01.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Tx01.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.36s] -Masking queries... [0.364s] -Building query seed set... [0.057s] -Algorithm: Double-indexed -Building query histograms... [0.136s] -Allocating buffers... [0s] -Loading reference sequences... [1.097s] -Masking reference... [0.692s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.31s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.235s] -Building query seed array... [0.103s] -Computing hash join... [0.097s] -Building seed filter... [0.005s] -Searching alignments... [0.168s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.241s] -Building query seed array... [0.097s] -Computing hash join... [0.086s] -Building seed filter... [0.006s] -Searching alignments... [0.144s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.254s] -Building query seed array... [0.099s] -Computing hash join... [0.083s] -Building seed filter... [0.006s] -Searching alignments... [0.139s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.211s] -Building query seed array... [0.086s] -Computing hash join... [0.084s] -Building seed filter... [0.007s] -Searching alignments... [0.151s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.211s] -Building query seed array... [0.081s] -Computing hash join... [0.082s] -Building seed filter... [0.005s] -Searching alignments... [0.124s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.238s] -Building query seed array... [0.1s] -Computing hash join... [0.083s] -Building seed filter... [0.005s] -Searching alignments... [0.126s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.248s] -Building query seed array... [0.101s] -Computing hash join... [0.082s] -Building seed filter... [0.005s] -Searching alignments... [0.123s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.204s] -Building query seed array... [0.083s] -Computing hash join... [0.081s] -Building seed filter... [0.006s] -Searching alignments... [0.122s] -Deallocating buffers... [0.054s] -Computing alignments... [1.626s] -Deallocating reference... [0.022s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.014s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.204s -Reported 11831 pairwise alignments, 11836 HSPs. -11831 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.353s] -Masking queries... [0.399s] -Building query seed set... [0.057s] -Algorithm: Double-indexed -Building query histograms... [0.136s] -Allocating buffers... [0s] -Loading reference sequences... [0.991s] -Masking reference... [0.629s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.301s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.215s] -Building query seed array... [0.098s] -Computing hash join... [0.106s] -Building seed filter... [0.005s] -Searching alignments... [0.227s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.226s] -Building query seed array... [0.093s] -Computing hash join... [0.078s] -Building seed filter... [0.006s] -Searching alignments... [0.231s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.234s] -Building query seed array... [0.097s] -Computing hash join... [0.079s] -Building seed filter... [0.006s] -Searching alignments... [0.208s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.194s] -Building query seed array... [0.101s] -Computing hash join... [0.083s] -Building seed filter... [0.006s] -Searching alignments... [0.223s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.196s] -Building query seed array... [0.089s] -Computing hash join... [0.078s] -Building seed filter... [0.006s] -Searching alignments... [0.206s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.223s] -Building query seed array... [0.109s] -Computing hash join... [0.079s] -Building seed filter... [0.006s] -Searching alignments... [0.194s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.235s] -Building query seed array... [0.101s] -Computing hash join... [0.076s] -Building seed filter... [0.006s] -Searching alignments... [0.184s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.196s] -Building query seed array... [0.089s] -Computing hash join... [0.076s] -Building seed filter... [0.006s] -Searching alignments... [0.179s] -Deallocating buffers... [0.051s] -Computing alignments... [2.893s] -Deallocating reference... [0.02s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.014s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.754s -Reported 28648 pairwise alignments, 28728 HSPs. -28648 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01/Sr_rh_Tx01_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Tx01_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn07.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn07.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.584s] -Masking queries... [0.4s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.149s] -Allocating buffers... [0s] -Loading reference sequences... [1.076s] -Masking reference... [0.7s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.299s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.239s] -Building query seed array... [0.125s] -Computing hash join... [0.121s] -Building seed filter... [0.008s] -Searching alignments... [0.174s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.243s] -Building query seed array... [0.113s] -Computing hash join... [0.102s] -Building seed filter... [0.009s] -Searching alignments... [0.16s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.25s] -Building query seed array... [0.115s] -Computing hash join... [0.104s] -Building seed filter... [0.007s] -Searching alignments... [0.164s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.097s] -Computing hash join... [0.102s] -Building seed filter... [0.007s] -Searching alignments... [0.166s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.21s] -Building query seed array... [0.105s] -Computing hash join... [0.104s] -Building seed filter... [0.007s] -Searching alignments... [0.15s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.236s] -Building query seed array... [0.112s] -Computing hash join... [0.101s] -Building seed filter... [0.008s] -Searching alignments... [0.147s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.25s] -Building query seed array... [0.12s] -Computing hash join... [0.101s] -Building seed filter... [0.007s] -Searching alignments... [0.146s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.209s] -Building query seed array... [0.097s] -Computing hash join... [0.097s] -Building seed filter... [0.007s] -Searching alignments... [0.142s] -Deallocating buffers... [0.058s] -Computing alignments... [1.725s] -Deallocating reference... [0.022s] -Loading reference sequences... [0s] -Deallocating buffers... [0.019s] -Deallocating queries... [0.015s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.006s -Reported 16673 pairwise alignments, 16752 HSPs. -16673 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.596s] -Masking queries... [0.392s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.148s] -Allocating buffers... [0s] -Loading reference sequences... [0.977s] -Masking reference... [0.637s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.274s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.211s] -Building query seed array... [0.116s] -Computing hash join... [0.107s] -Building seed filter... [0.009s] -Searching alignments... [0.422s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.223s] -Building query seed array... [0.114s] -Computing hash join... [0.096s] -Building seed filter... [0.009s] -Searching alignments... [0.35s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.235s] -Building query seed array... [0.118s] -Computing hash join... [0.095s] -Building seed filter... [0.009s] -Searching alignments... [0.287s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.196s] -Building query seed array... [0.102s] -Computing hash join... [0.095s] -Building seed filter... [0.009s] -Searching alignments... [0.318s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.199s] -Building query seed array... [0.098s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.304s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.223s] -Building query seed array... [0.109s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.286s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.236s] -Building query seed array... [0.115s] -Computing hash join... [0.096s] -Building seed filter... [0.008s] -Searching alignments... [0.25s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.199s] -Building query seed array... [0.101s] -Computing hash join... [0.095s] -Building seed filter... [0.008s] -Searching alignments... [0.277s] -Deallocating buffers... [0.049s] -Computing alignments... [3.133s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.019s] -Deallocating queries... [0.018s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.276s -Reported 35577 pairwise alignments, 35833 HSPs. -35577 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07/Sr_rh_Nn07_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn07_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn01.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn01.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.35s] -Masking queries... [0.382s] -Building query seed set... [0.04s] -Algorithm: Double-indexed -Building query histograms... [0.144s] -Allocating buffers... [0s] -Loading reference sequences... [1.137s] -Masking reference... [0.713s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.301s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.239s] -Building query seed array... [0.106s] -Computing hash join... [0.124s] -Building seed filter... [0.009s] -Searching alignments... [0.156s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.239s] -Building query seed array... [0.102s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.152s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.253s] -Building query seed array... [0.112s] -Computing hash join... [0.099s] -Building seed filter... [0.008s] -Searching alignments... [0.162s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.209s] -Building query seed array... [0.098s] -Computing hash join... [0.099s] -Building seed filter... [0.007s] -Searching alignments... [0.153s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.21s] -Building query seed array... [0.102s] -Computing hash join... [0.097s] -Building seed filter... [0.008s] -Searching alignments... [0.14s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.236s] -Building query seed array... [0.111s] -Computing hash join... [0.099s] -Building seed filter... [0.008s] -Searching alignments... [0.14s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.247s] -Building query seed array... [0.11s] -Computing hash join... [0.1s] -Building seed filter... [0.008s] -Searching alignments... [0.142s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.102s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.147s] -Deallocating buffers... [0.059s] -Computing alignments... [1.749s] -Deallocating reference... [0.022s] -Loading reference sequences... [0s] -Deallocating buffers... [0.023s] -Deallocating queries... [0.018s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.738s -Reported 16335 pairwise alignments, 16447 HSPs. -16335 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.37s] -Masking queries... [0.377s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.163s] -Allocating buffers... [0s] -Loading reference sequences... [1.004s] -Masking reference... [0.651s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.275s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.217s] -Building query seed array... [0.111s] -Computing hash join... [0.109s] -Building seed filter... [0.007s] -Searching alignments... [0.411s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.228s] -Building query seed array... [0.105s] -Computing hash join... [0.089s] -Building seed filter... [0.007s] -Searching alignments... [0.346s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.106s] -Computing hash join... [0.092s] -Building seed filter... [0.007s] -Searching alignments... [0.337s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.197s] -Building query seed array... [0.093s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.366s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.202s] -Building query seed array... [0.097s] -Computing hash join... [0.088s] -Building seed filter... [0.007s] -Searching alignments... [0.276s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.227s] -Building query seed array... [0.106s] -Computing hash join... [0.088s] -Building seed filter... [0.006s] -Searching alignments... [0.262s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.238s] -Building query seed array... [0.117s] -Computing hash join... [0.092s] -Building seed filter... [0.006s] -Searching alignments... [0.237s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.212s] -Building query seed array... [0.099s] -Computing hash join... [0.091s] -Building seed filter... [0.007s] -Searching alignments... [0.239s] -Deallocating buffers... [0.051s] -Computing alignments... [3.114s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.016s] -Deallocating queries... [0.019s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.004s -Reported 34435 pairwise alignments, 34792 HSPs. -34435 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01/Sr_rh_Nn01_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn01_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Bv04.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Bv04.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.941s] -Masking queries... [0.466s] -Building query seed set... [0.05s] -Algorithm: Double-indexed -Building query histograms... [0.161s] -Allocating buffers... [0s] -Loading reference sequences... [1.227s] -Masking reference... [0.695s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.309s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.228s] -Building query seed array... [0.124s] -Computing hash join... [0.118s] -Building seed filter... [0.007s] -Searching alignments... [0.178s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.241s] -Building query seed array... [0.115s] -Computing hash join... [0.096s] -Building seed filter... [0.008s] -Searching alignments... [0.183s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.25s] -Building query seed array... [0.116s] -Computing hash join... [0.099s] -Building seed filter... [0.008s] -Searching alignments... [0.18s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.215s] -Building query seed array... [0.102s] -Computing hash join... [0.099s] -Building seed filter... [0.008s] -Searching alignments... [0.183s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.213s] -Building query seed array... [0.105s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.159s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.238s] -Building query seed array... [0.114s] -Computing hash join... [0.099s] -Building seed filter... [0.008s] -Searching alignments... [0.156s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.247s] -Building query seed array... [0.117s] -Computing hash join... [0.095s] -Building seed filter... [0.007s] -Searching alignments... [0.155s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.108s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.15s] -Deallocating buffers... [0.057s] -Computing alignments... [1.629s] -Deallocating reference... [0.023s] -Loading reference sequences... [0s] -Deallocating buffers... [0.017s] -Deallocating queries... [0.022s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.591s -Reported 16731 pairwise alignments, 16862 HSPs. -16731 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.937s] -Masking queries... [0.481s] -Building query seed set... [0.051s] -Algorithm: Double-indexed -Building query histograms... [0.175s] -Allocating buffers... [0s] -Loading reference sequences... [0.984s] -Masking reference... [0.641s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.275s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.218s] -Building query seed array... [0.129s] -Computing hash join... [0.112s] -Building seed filter... [0.01s] -Searching alignments... [0.36s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.226s] -Building query seed array... [0.114s] -Computing hash join... [0.093s] -Building seed filter... [0.008s] -Searching alignments... [0.31s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.236s] -Building query seed array... [0.116s] -Computing hash join... [0.093s] -Building seed filter... [0.008s] -Searching alignments... [0.265s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.2s] -Building query seed array... [0.108s] -Computing hash join... [0.093s] -Building seed filter... [0.008s] -Searching alignments... [0.322s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.197s] -Building query seed array... [0.11s] -Computing hash join... [0.091s] -Building seed filter... [0.008s] -Searching alignments... [0.261s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.229s] -Building query seed array... [0.116s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.249s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.236s] -Building query seed array... [0.124s] -Computing hash join... [0.091s] -Building seed filter... [0.008s] -Searching alignments... [0.248s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.2s] -Building query seed array... [0.107s] -Computing hash join... [0.088s] -Building seed filter... [0.007s] -Searching alignments... [0.237s] -Deallocating buffers... [0.052s] -Computing alignments... [3.118s] -Deallocating reference... [0.014s] -Loading reference sequences... [0s] -Deallocating buffers... [0.017s] -Deallocating queries... [0.017s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.541s -Reported 33330 pairwise alignments, 33675 HSPs. -33330 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04/Sr_rh_Bv04_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Bv04_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Usac.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Usac.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.916s] -Masking queries... [0.261s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.109s] -Allocating buffers... [0s] -Loading reference sequences... [1.093s] -Masking reference... [0.695s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.298s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.236s] -Building query seed array... [0.087s] -Computing hash join... [0.124s] -Building seed filter... [0.006s] -Searching alignments... [0.147s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.245s] -Building query seed array... [0.08s] -Computing hash join... [0.1s] -Building seed filter... [0.007s] -Searching alignments... [0.138s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.251s] -Building query seed array... [0.084s] -Computing hash join... [0.097s] -Building seed filter... [0.008s] -Searching alignments... [0.147s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.215s] -Building query seed array... [0.071s] -Computing hash join... [0.095s] -Building seed filter... [0.007s] -Searching alignments... [0.139s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.21s] -Building query seed array... [0.074s] -Computing hash join... [0.103s] -Building seed filter... [0.006s] -Searching alignments... [0.127s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.235s] -Building query seed array... [0.076s] -Computing hash join... [0.097s] -Building seed filter... [0.006s] -Searching alignments... [0.123s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.245s] -Building query seed array... [0.08s] -Computing hash join... [0.099s] -Building seed filter... [0.007s] -Searching alignments... [0.122s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.208s] -Building query seed array... [0.065s] -Computing hash join... [0.097s] -Building seed filter... [0.007s] -Searching alignments... [0.121s] -Deallocating buffers... [0.054s] -Computing alignments... [1.485s] -Deallocating reference... [0.019s] -Loading reference sequences... [0s] -Deallocating buffers... [0.013s] -Deallocating queries... [0.013s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.432s -Reported 18730 pairwise alignments, 18769 HSPs. -18730 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.923s] -Masking queries... [0.263s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.098s] -Allocating buffers... [0s] -Loading reference sequences... [0.988s] -Masking reference... [0.64s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.269s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.221s] -Building query seed array... [0.087s] -Computing hash join... [0.107s] -Building seed filter... [0.007s] -Searching alignments... [0.263s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.24s] -Building query seed array... [0.083s] -Computing hash join... [0.1s] -Building seed filter... [0.006s] -Searching alignments... [0.253s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.236s] -Building query seed array... [0.087s] -Computing hash join... [0.097s] -Building seed filter... [0.008s] -Searching alignments... [0.231s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.2s] -Building query seed array... [0.069s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.255s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.203s] -Building query seed array... [0.072s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.217s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.222s] -Building query seed array... [0.077s] -Computing hash join... [0.093s] -Building seed filter... [0.007s] -Searching alignments... [0.178s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.239s] -Building query seed array... [0.087s] -Computing hash join... [0.097s] -Building seed filter... [0.005s] -Searching alignments... [0.181s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.193s] -Building query seed array... [0.071s] -Computing hash join... [0.092s] -Building seed filter... [0.006s] -Searching alignments... [0.177s] -Deallocating buffers... [0.053s] -Computing alignments... [2.193s] -Deallocating reference... [0.018s] -Loading reference sequences... [0s] -Deallocating buffers... [0.012s] -Deallocating queries... [0.012s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.523s -Reported 40730 pairwise alignments, 40859 HSPs. -40730 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac/Sr_rh_Usac_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Usac_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn04.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn04.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [2.191s] -Masking queries... [0.615s] -Building query seed set... [0.04s] -Algorithm: Double-indexed -Building query histograms... [0.201s] -Allocating buffers... [0s] -Loading reference sequences... [1.266s] -Masking reference... [0.692s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.331s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.231s] -Building query seed array... [0.161s] -Computing hash join... [0.135s] -Building seed filter... [0.009s] -Searching alignments... [0.231s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.249s] -Building query seed array... [0.148s] -Computing hash join... [0.111s] -Building seed filter... [0.009s] -Searching alignments... [0.197s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.247s] -Building query seed array... [0.156s] -Computing hash join... [0.112s] -Building seed filter... [0.009s] -Searching alignments... [0.205s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.213s] -Building query seed array... [0.135s] -Computing hash join... [0.112s] -Building seed filter... [0.009s] -Searching alignments... [0.207s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.212s] -Building query seed array... [0.136s] -Computing hash join... [0.115s] -Building seed filter... [0.014s] -Searching alignments... [0.192s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.246s] -Building query seed array... [0.153s] -Computing hash join... [0.12s] -Building seed filter... [0.009s] -Searching alignments... [0.183s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.252s] -Building query seed array... [0.155s] -Computing hash join... [0.109s] -Building seed filter... [0.008s] -Searching alignments... [0.198s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.215s] -Building query seed array... [0.135s] -Computing hash join... [0.118s] -Building seed filter... [0.008s] -Searching alignments... [0.181s] -Deallocating buffers... [0.059s] -Computing alignments... [2.565s] -Deallocating reference... [0.02s] -Loading reference sequences... [0s] -Deallocating buffers... [0.023s] -Deallocating queries... [0.021s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.715s -Reported 27246 pairwise alignments, 27470 HSPs. -27246 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [2.212s] -Masking queries... [0.606s] -Building query seed set... [0.041s] -Algorithm: Double-indexed -Building query histograms... [0.199s] -Allocating buffers... [0s] -Loading reference sequences... [1.006s] -Masking reference... [0.651s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.285s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.217s] -Building query seed array... [0.152s] -Computing hash join... [0.111s] -Building seed filter... [0.007s] -Searching alignments... [0.637s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.246s] -Building query seed array... [0.156s] -Computing hash join... [0.104s] -Building seed filter... [0.01s] -Searching alignments... [0.491s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.231s] -Building query seed array... [0.15s] -Computing hash join... [0.106s] -Building seed filter... [0.009s] -Searching alignments... [0.405s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.194s] -Building query seed array... [0.13s] -Computing hash join... [0.101s] -Building seed filter... [0.007s] -Searching alignments... [0.545s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.198s] -Building query seed array... [0.132s] -Computing hash join... [0.101s] -Building seed filter... [0.009s] -Searching alignments... [0.449s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.224s] -Building query seed array... [0.151s] -Computing hash join... [0.1s] -Building seed filter... [0.01s] -Searching alignments... [0.443s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.235s] -Building query seed array... [0.153s] -Computing hash join... [0.103s] -Building seed filter... [0.01s] -Searching alignments... [0.358s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.196s] -Building query seed array... [0.144s] -Computing hash join... [0.103s] -Building seed filter... [0.008s] -Searching alignments... [0.407s] -Deallocating buffers... [0.052s] -Computing alignments... [4.479s] -Deallocating reference... [0.014s] -Loading reference sequences... [0s] -Deallocating buffers... [0.024s] -Deallocating queries... [0.022s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 17.183s -Reported 56655 pairwise alignments, 57309 HSPs. -56655 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04/Sr_rh_Nn04_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn04_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Emar.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Emar.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.531s] -Masking queries... [0.153s] -Building query seed set... [0.04s] -Algorithm: Double-indexed -Building query histograms... [0.07s] -Allocating buffers... [0s] -Loading reference sequences... [1.189s] -Masking reference... [0.687s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.301s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.229s] -Building query seed array... [0.057s] -Computing hash join... [0.121s] -Building seed filter... [0.005s] -Searching alignments... [0.079s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.239s] -Building query seed array... [0.054s] -Computing hash join... [0.088s] -Building seed filter... [0.004s] -Searching alignments... [0.078s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.251s] -Building query seed array... [0.059s] -Computing hash join... [0.085s] -Building seed filter... [0.006s] -Searching alignments... [0.071s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.204s] -Building query seed array... [0.047s] -Computing hash join... [0.079s] -Building seed filter... [0.006s] -Searching alignments... [0.068s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.206s] -Building query seed array... [0.053s] -Computing hash join... [0.083s] -Building seed filter... [0.005s] -Searching alignments... [0.075s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.238s] -Building query seed array... [0.059s] -Computing hash join... [0.085s] -Building seed filter... [0.005s] -Searching alignments... [0.067s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.243s] -Building query seed array... [0.054s] -Computing hash join... [0.08s] -Building seed filter... [0.005s] -Searching alignments... [0.069s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.212s] -Building query seed array... [0.059s] -Computing hash join... [0.087s] -Building seed filter... [0.005s] -Searching alignments... [0.065s] -Deallocating buffers... [0.056s] -Computing alignments... [0.634s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.005s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 7.328s -Reported 5342 pairwise alignments, 5400 HSPs. -5342 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.534s] -Masking queries... [0.167s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.067s] -Allocating buffers... [0s] -Loading reference sequences... [0.981s] -Masking reference... [0.636s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.274s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.221s] -Building query seed array... [0.067s] -Computing hash join... [0.105s] -Building seed filter... [0.005s] -Searching alignments... [0.102s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.246s] -Building query seed array... [0.064s] -Computing hash join... [0.082s] -Building seed filter... [0.005s] -Searching alignments... [0.101s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.237s] -Building query seed array... [0.056s] -Computing hash join... [0.08s] -Building seed filter... [0.005s] -Searching alignments... [0.092s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.192s] -Building query seed array... [0.052s] -Computing hash join... [0.08s] -Building seed filter... [0.005s] -Searching alignments... [0.097s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.191s] -Building query seed array... [0.051s] -Computing hash join... [0.076s] -Building seed filter... [0.005s] -Searching alignments... [0.085s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.216s] -Building query seed array... [0.057s] -Computing hash join... [0.081s] -Building seed filter... [0.006s] -Searching alignments... [0.083s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.056s] -Computing hash join... [0.08s] -Building seed filter... [0.005s] -Searching alignments... [0.08s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.192s] -Building query seed array... [0.043s] -Computing hash join... [0.078s] -Building seed filter... [0.005s] -Searching alignments... [0.087s] -Deallocating buffers... [0.051s] -Computing alignments... [1.093s] -Deallocating reference... [0.017s] -Loading reference sequences... [0s] -Deallocating buffers... [0.008s] -Deallocating queries... [0.008s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 7.522s -Reported 11056 pairwise alignments, 11214 HSPs. -11056 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar/Sr_rh_Emar_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Emar_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Rsp1.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Rsp1.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.033s] -Masking queries... [0.559s] -Building query seed set... [0.049s] -Algorithm: Double-indexed -Building query histograms... [0.094s] -Allocating buffers... [0s] -Loading reference sequences... [1.11s] -Masking reference... [0.694s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.319s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.232s] -Building query seed array... [0.075s] -Computing hash join... [0.125s] -Building seed filter... [0.007s] -Searching alignments... [0.126s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.243s] -Building query seed array... [0.065s] -Computing hash join... [0.105s] -Building seed filter... [0.005s] -Searching alignments... [0.115s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.249s] -Building query seed array... [0.075s] -Computing hash join... [0.104s] -Building seed filter... [0.005s] -Searching alignments... [0.118s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.217s] -Building query seed array... [0.077s] -Computing hash join... [0.1s] -Building seed filter... [0.005s] -Searching alignments... [0.115s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.223s] -Building query seed array... [0.063s] -Computing hash join... [0.091s] -Building seed filter... [0.005s] -Searching alignments... [0.098s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.239s] -Building query seed array... [0.069s] -Computing hash join... [0.097s] -Building seed filter... [0.005s] -Searching alignments... [0.1s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.244s] -Building query seed array... [0.069s] -Computing hash join... [0.092s] -Building seed filter... [0.005s] -Searching alignments... [0.1s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.206s] -Building query seed array... [0.059s] -Computing hash join... [0.091s] -Building seed filter... [0.005s] -Searching alignments... [0.097s] -Deallocating buffers... [0.058s] -Computing alignments... [1.22s] -Deallocating reference... [0.019s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.012s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.348s -Reported 17091 pairwise alignments, 17125 HSPs. -17091 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.034s] -Masking queries... [0.266s] -Building query seed set... [0.049s] -Algorithm: Double-indexed -Building query histograms... [0.093s] -Allocating buffers... [0s] -Loading reference sequences... [0.989s] -Masking reference... [0.658s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.292s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.222s] -Building query seed array... [0.079s] -Computing hash join... [0.132s] -Building seed filter... [0.005s] -Searching alignments... [0.202s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.227s] -Building query seed array... [0.069s] -Computing hash join... [0.1s] -Building seed filter... [0.006s] -Searching alignments... [0.201s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.238s] -Building query seed array... [0.067s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.174s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.2s] -Building query seed array... [0.064s] -Computing hash join... [0.093s] -Building seed filter... [0.006s] -Searching alignments... [0.181s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.199s] -Building query seed array... [0.058s] -Computing hash join... [0.088s] -Building seed filter... [0.005s] -Searching alignments... [0.174s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.223s] -Building query seed array... [0.065s] -Computing hash join... [0.092s] -Building seed filter... [0.005s] -Searching alignments... [0.177s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.228s] -Building query seed array... [0.065s] -Computing hash join... [0.088s] -Building seed filter... [0.005s] -Searching alignments... [0.154s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.194s] -Building query seed array... [0.062s] -Computing hash join... [0.087s] -Building seed filter... [0.005s] -Searching alignments... [0.154s] -Deallocating buffers... [0.052s] -Computing alignments... [2.101s] -Deallocating reference... [0.019s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.009s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.112s -Reported 36259 pairwise alignments, 36348 HSPs. -36259 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1/Sr_rh_Rsp1_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Rsp1_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Sspa.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Sspa.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.778s] -Masking queries... [0.215s] -Building query seed set... [0.043s] -Algorithm: Double-indexed -Building query histograms... [0.081s] -Allocating buffers... [0s] -Loading reference sequences... [1.097s] -Masking reference... [0.696s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.303s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.232s] -Building query seed array... [0.068s] -Computing hash join... [0.132s] -Building seed filter... [0.006s] -Searching alignments... [0.112s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.24s] -Building query seed array... [0.062s] -Computing hash join... [0.108s] -Building seed filter... [0.006s] -Searching alignments... [0.117s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.256s] -Building query seed array... [0.064s] -Computing hash join... [0.101s] -Building seed filter... [0.006s] -Searching alignments... [0.105s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.211s] -Building query seed array... [0.054s] -Computing hash join... [0.098s] -Building seed filter... [0.006s] -Searching alignments... [0.107s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.219s] -Building query seed array... [0.054s] -Computing hash join... [0.094s] -Building seed filter... [0.005s] -Searching alignments... [0.1s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.245s] -Building query seed array... [0.068s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.099s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.256s] -Building query seed array... [0.065s] -Computing hash join... [0.092s] -Building seed filter... [0.006s] -Searching alignments... [0.093s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.206s] -Building query seed array... [0.057s] -Computing hash join... [0.095s] -Building seed filter... [0.005s] -Searching alignments... [0.098s] -Deallocating buffers... [0.056s] -Computing alignments... [1.085s] -Deallocating reference... [0.019s] -Loading reference sequences... [0s] -Deallocating buffers... [0.008s] -Deallocating queries... [0.009s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 8.486s -Reported 10845 pairwise alignments, 10920 HSPs. -10845 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.783s] -Masking queries... [0.228s] -Building query seed set... [0.043s] -Algorithm: Double-indexed -Building query histograms... [0.081s] -Allocating buffers... [0s] -Loading reference sequences... [0.979s] -Masking reference... [0.641s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.291s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.219s] -Building query seed array... [0.07s] -Computing hash join... [0.109s] -Building seed filter... [0.005s] -Searching alignments... [0.151s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.222s] -Building query seed array... [0.058s] -Computing hash join... [0.096s] -Building seed filter... [0.005s] -Searching alignments... [0.15s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.23s] -Building query seed array... [0.066s] -Computing hash join... [0.093s] -Building seed filter... [0.006s] -Searching alignments... [0.135s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.198s] -Building query seed array... [0.056s] -Computing hash join... [0.093s] -Building seed filter... [0.005s] -Searching alignments... [0.144s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.193s] -Building query seed array... [0.055s] -Computing hash join... [0.088s] -Building seed filter... [0.006s] -Searching alignments... [0.124s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.224s] -Building query seed array... [0.057s] -Computing hash join... [0.088s] -Building seed filter... [0.006s] -Searching alignments... [0.132s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.231s] -Building query seed array... [0.061s] -Computing hash join... [0.087s] -Building seed filter... [0.006s] -Searching alignments... [0.125s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.195s] -Building query seed array... [0.056s] -Computing hash join... [0.089s] -Building seed filter... [0.006s] -Searching alignments... [0.119s] -Deallocating buffers... [0.05s] -Computing alignments... [1.576s] -Deallocating reference... [0.018s] -Loading reference sequences... [0s] -Deallocating buffers... [0.009s] -Deallocating queries... [0.011s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 8.814s -Reported 23074 pairwise alignments, 23301 HSPs. -23074 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa/Sr_rh_Sspa_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Sspa_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Hhir.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Hhir.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.628s] -Masking queries... [0.179s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.08s] -Allocating buffers... [0s] -Loading reference sequences... [1.105s] -Masking reference... [0.806s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.304s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.241s] -Building query seed array... [0.061s] -Computing hash join... [0.107s] -Building seed filter... [0.006s] -Searching alignments... [0.111s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.243s] -Building query seed array... [0.055s] -Computing hash join... [0.084s] -Building seed filter... [0.005s] -Searching alignments... [0.079s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.251s] -Building query seed array... [0.056s] -Computing hash join... [0.077s] -Building seed filter... [0.005s] -Searching alignments... [0.081s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.213s] -Building query seed array... [0.053s] -Computing hash join... [0.078s] -Building seed filter... [0.005s] -Searching alignments... [0.084s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.211s] -Building query seed array... [0.055s] -Computing hash join... [0.076s] -Building seed filter... [0.005s] -Searching alignments... [0.072s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.238s] -Building query seed array... [0.053s] -Computing hash join... [0.074s] -Building seed filter... [0.005s] -Searching alignments... [0.081s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.251s] -Building query seed array... [0.057s] -Computing hash join... [0.074s] -Building seed filter... [0.005s] -Searching alignments... [0.079s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.212s] -Building query seed array... [0.055s] -Computing hash join... [0.077s] -Building seed filter... [0.004s] -Searching alignments... [0.074s] -Deallocating buffers... [0.056s] -Computing alignments... [0.796s] -Deallocating reference... [0.023s] -Loading reference sequences... [0s] -Deallocating buffers... [0.006s] -Deallocating queries... [0.007s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 7.726s -Reported 6766 pairwise alignments, 6777 HSPs. -6766 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.632s] -Masking queries... [0.235s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.074s] -Allocating buffers... [0s] -Loading reference sequences... [1.024s] -Masking reference... [1.658s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.282s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.222s] -Building query seed array... [0.067s] -Computing hash join... [0.097s] -Building seed filter... [0.006s] -Searching alignments... [0.12s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.223s] -Building query seed array... [0.054s] -Computing hash join... [0.081s] -Building seed filter... [0.005s] -Searching alignments... [0.112s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.232s] -Building query seed array... [0.059s] -Computing hash join... [0.075s] -Building seed filter... [0.005s] -Searching alignments... [0.107s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.196s] -Building query seed array... [0.05s] -Computing hash join... [0.076s] -Building seed filter... [0.006s] -Searching alignments... [0.114s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.195s] -Building query seed array... [0.054s] -Computing hash join... [0.076s] -Building seed filter... [0.004s] -Searching alignments... [0.101s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.221s] -Building query seed array... [0.054s] -Computing hash join... [0.07s] -Building seed filter... [0.005s] -Searching alignments... [0.099s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.227s] -Building query seed array... [0.06s] -Computing hash join... [0.072s] -Building seed filter... [0.005s] -Searching alignments... [0.101s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.192s] -Building query seed array... [0.05s] -Computing hash join... [0.071s] -Building seed filter... [0.005s] -Searching alignments... [0.091s] -Deallocating buffers... [0.053s] -Computing alignments... [1.324s] -Deallocating reference... [0.025s] -Loading reference sequences... [0s] -Deallocating buffers... [0.006s] -Deallocating queries... [0.01s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.073s -Reported 14202 pairwise alignments, 14244 HSPs. -14202 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir/Sr_rh_Hhir_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Hhir_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn12.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn12.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.207s] -Masking queries... [0.31s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.142s] -Allocating buffers... [0s] -Loading reference sequences... [1.123s] -Masking reference... [0.708s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.292s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.227s] -Building query seed array... [0.1s] -Computing hash join... [0.109s] -Building seed filter... [0.005s] -Searching alignments... [0.135s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.24s] -Building query seed array... [0.095s] -Computing hash join... [0.097s] -Building seed filter... [0.006s] -Searching alignments... [0.127s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.251s] -Building query seed array... [0.092s] -Computing hash join... [0.097s] -Building seed filter... [0.006s] -Searching alignments... [0.132s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.213s] -Building query seed array... [0.084s] -Computing hash join... [0.096s] -Building seed filter... [0.005s] -Searching alignments... [0.128s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.212s] -Building query seed array... [0.084s] -Computing hash join... [0.095s] -Building seed filter... [0.007s] -Searching alignments... [0.119s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.238s] -Building query seed array... [0.092s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.116s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.251s] -Building query seed array... [0.097s] -Computing hash join... [0.097s] -Building seed filter... [0.007s] -Searching alignments... [0.122s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.211s] -Building query seed array... [0.088s] -Computing hash join... [0.099s] -Building seed filter... [0.008s] -Searching alignments... [0.116s] -Deallocating buffers... [0.056s] -Computing alignments... [1.169s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0.013s] -Deallocating queries... [0.012s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.541s -Reported 12180 pairwise alignments, 12261 HSPs. -12180 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.216s] -Masking queries... [0.327s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.124s] -Allocating buffers... [0s] -Loading reference sequences... [0.989s] -Masking reference... [0.637s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.275s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.222s] -Building query seed array... [0.091s] -Computing hash join... [0.096s] -Building seed filter... [0.005s] -Searching alignments... [0.209s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.23s] -Building query seed array... [0.099s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.195s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.103s] -Computing hash join... [0.089s] -Building seed filter... [0.006s] -Searching alignments... [0.178s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.192s] -Building query seed array... [0.084s] -Computing hash join... [0.091s] -Building seed filter... [0.006s] -Searching alignments... [0.179s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.196s] -Building query seed array... [0.089s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.168s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.247s] -Building query seed array... [0.115s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.175s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.097s] -Computing hash join... [0.087s] -Building seed filter... [0.007s] -Searching alignments... [0.166s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.191s] -Building query seed array... [0.09s] -Computing hash join... [0.092s] -Building seed filter... [0.007s] -Searching alignments... [0.159s] -Deallocating buffers... [0.053s] -Computing alignments... [2.15s] -Deallocating reference... [0.017s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.013s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.621s -Reported 26508 pairwise alignments, 26714 HSPs. -26508 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12/Sr_rh_Nn12_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn12_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn14.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn14.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.174s] -Masking queries... [0.328s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.13s] -Allocating buffers... [0s] -Loading reference sequences... [1.103s] -Masking reference... [0.708s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.315s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.238s] -Building query seed array... [0.101s] -Computing hash join... [0.11s] -Building seed filter... [0.007s] -Searching alignments... [0.135s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.239s] -Building query seed array... [0.093s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.128s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.25s] -Building query seed array... [0.093s] -Computing hash join... [0.097s] -Building seed filter... [0.006s] -Searching alignments... [0.131s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.208s] -Building query seed array... [0.087s] -Computing hash join... [0.097s] -Building seed filter... [0.006s] -Searching alignments... [0.129s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.209s] -Building query seed array... [0.085s] -Computing hash join... [0.098s] -Building seed filter... [0.006s] -Searching alignments... [0.121s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.249s] -Building query seed array... [0.099s] -Computing hash join... [0.095s] -Building seed filter... [0.005s] -Searching alignments... [0.122s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.245s] -Building query seed array... [0.093s] -Computing hash join... [0.098s] -Building seed filter... [0.006s] -Searching alignments... [0.12s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.209s] -Building query seed array... [0.078s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.115s] -Deallocating buffers... [0.058s] -Computing alignments... [1.155s] -Deallocating reference... [0.02s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.015s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.521s -Reported 12561 pairwise alignments, 12646 HSPs. -12561 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.193s] -Masking queries... [0.313s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.136s] -Allocating buffers... [0s] -Loading reference sequences... [1.003s] -Masking reference... [0.644s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.283s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.217s] -Building query seed array... [0.093s] -Computing hash join... [0.096s] -Building seed filter... [0.008s] -Searching alignments... [0.331s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.223s] -Building query seed array... [0.099s] -Computing hash join... [0.091s] -Building seed filter... [0.007s] -Searching alignments... [0.196s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.232s] -Building query seed array... [0.099s] -Computing hash join... [0.087s] -Building seed filter... [0.007s] -Searching alignments... [0.179s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.198s] -Building query seed array... [0.082s] -Computing hash join... [0.089s] -Building seed filter... [0.007s] -Searching alignments... [0.174s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.195s] -Building query seed array... [0.093s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.155s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.218s] -Building query seed array... [0.097s] -Computing hash join... [0.093s] -Building seed filter... [0.007s] -Searching alignments... [0.161s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.231s] -Building query seed array... [0.097s] -Computing hash join... [0.087s] -Building seed filter... [0.007s] -Searching alignments... [0.159s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.196s] -Building query seed array... [0.083s] -Computing hash join... [0.088s] -Building seed filter... [0.007s] -Searching alignments... [0.158s] -Deallocating buffers... [0.049s] -Computing alignments... [2.103s] -Deallocating reference... [0.023s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.016s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.601s -Reported 27283 pairwise alignments, 27554 HSPs. -27283 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14/Sr_rh_Nn14_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn14_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Gl02.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Gl02.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [2.204s] -Masking queries... [0.607s] -Building query seed set... [0.04s] -Algorithm: Double-indexed -Building query histograms... [0.22s] -Allocating buffers... [0s] -Loading reference sequences... [1.093s] -Masking reference... [0.691s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.31s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.236s] -Building query seed array... [0.156s] -Computing hash join... [0.138s] -Building seed filter... [0.01s] -Searching alignments... [0.229s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.245s] -Building query seed array... [0.146s] -Computing hash join... [0.11s] -Building seed filter... [0.012s] -Searching alignments... [0.227s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.248s] -Building query seed array... [0.148s] -Computing hash join... [0.122s] -Building seed filter... [0.009s] -Searching alignments... [0.228s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.213s] -Building query seed array... [0.133s] -Computing hash join... [0.109s] -Building seed filter... [0.01s] -Searching alignments... [0.216s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.213s] -Building query seed array... [0.142s] -Computing hash join... [0.113s] -Building seed filter... [0.009s] -Searching alignments... [0.2s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.246s] -Building query seed array... [0.149s] -Computing hash join... [0.113s] -Building seed filter... [0.009s] -Searching alignments... [0.203s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.253s] -Building query seed array... [0.157s] -Computing hash join... [0.111s] -Building seed filter... [0.009s] -Searching alignments... [0.194s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.133s] -Computing hash join... [0.109s] -Building seed filter... [0.008s] -Searching alignments... [0.192s] -Deallocating buffers... [0.059s] -Computing alignments... [2.363s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0.024s] -Deallocating queries... [0.024s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.428s -Reported 23866 pairwise alignments, 23926 HSPs. -23866 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [2.219s] -Masking queries... [0.556s] -Building query seed set... [0.041s] -Algorithm: Double-indexed -Building query histograms... [0.203s] -Allocating buffers... [0s] -Loading reference sequences... [0.998s] -Masking reference... [0.642s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.287s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.214s] -Building query seed array... [0.154s] -Computing hash join... [0.112s] -Building seed filter... [0.01s] -Searching alignments... [0.337s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.227s] -Building query seed array... [0.153s] -Computing hash join... [0.106s] -Building seed filter... [0.011s] -Searching alignments... [0.315s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.235s] -Building query seed array... [0.158s] -Computing hash join... [0.104s] -Building seed filter... [0.008s] -Searching alignments... [0.305s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.222s] -Building query seed array... [0.142s] -Computing hash join... [0.109s] -Building seed filter... [0.007s] -Searching alignments... [0.315s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.212s] -Building query seed array... [0.135s] -Computing hash join... [0.103s] -Building seed filter... [0.01s] -Searching alignments... [0.271s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.223s] -Building query seed array... [0.152s] -Computing hash join... [0.105s] -Building seed filter... [0.01s] -Searching alignments... [0.287s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.23s] -Building query seed array... [0.154s] -Computing hash join... [0.109s] -Building seed filter... [0.009s] -Searching alignments... [0.271s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.195s] -Building query seed array... [0.139s] -Computing hash join... [0.106s] -Building seed filter... [0.01s] -Searching alignments... [0.261s] -Deallocating buffers... [0.049s] -Computing alignments... [4.193s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0.024s] -Deallocating queries... [0.028s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 15.549s -Reported 46583 pairwise alignments, 46748 HSPs. -46583 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02/Sr_rh_Gl02_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Gl02_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Bv05.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Bv05.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.826s] -Masking queries... [0.521s] -Building query seed set... [0.048s] -Algorithm: Double-indexed -Building query histograms... [0.15s] -Allocating buffers... [0s] -Loading reference sequences... [1.084s] -Masking reference... [0.692s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.299s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.236s] -Building query seed array... [0.124s] -Computing hash join... [0.115s] -Building seed filter... [0.007s] -Searching alignments... [0.182s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.242s] -Building query seed array... [0.111s] -Computing hash join... [0.095s] -Building seed filter... [0.008s] -Searching alignments... [0.174s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.255s] -Building query seed array... [0.113s] -Computing hash join... [0.098s] -Building seed filter... [0.008s] -Searching alignments... [0.171s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.212s] -Building query seed array... [0.098s] -Computing hash join... [0.097s] -Building seed filter... [0.009s] -Searching alignments... [0.174s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.21s] -Building query seed array... [0.101s] -Computing hash join... [0.098s] -Building seed filter... [0.008s] -Searching alignments... [0.163s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.241s] -Building query seed array... [0.108s] -Computing hash join... [0.095s] -Building seed filter... [0.006s] -Searching alignments... [0.15s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.247s] -Building query seed array... [0.112s] -Computing hash join... [0.097s] -Building seed filter... [0.007s] -Searching alignments... [0.152s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.208s] -Building query seed array... [0.098s] -Computing hash join... [0.096s] -Building seed filter... [0.009s] -Searching alignments... [0.147s] -Deallocating buffers... [0.06s] -Computing alignments... [1.576s] -Deallocating reference... [0.018s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.019s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.239s -Reported 16723 pairwise alignments, 16853 HSPs. -16723 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05/BvE -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.809s] -Masking queries... [0.438s] -Building query seed set... [0.048s] -Algorithm: Double-indexed -Building query histograms... [0.148s] -Allocating buffers... [0s] -Loading reference sequences... [0.987s] -Masking reference... [0.634s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.266s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.226s] -Building query seed array... [0.116s] -Computing hash join... [0.108s] -Building seed filter... [0.007s] -Searching alignments... [0.315s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.228s] -Building query seed array... [0.106s] -Computing hash join... [0.088s] -Building seed filter... [0.007s] -Searching alignments... [0.285s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.234s] -Building query seed array... [0.111s] -Computing hash join... [0.089s] -Building seed filter... [0.008s] -Searching alignments... [0.266s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.197s] -Building query seed array... [0.099s] -Computing hash join... [0.089s] -Building seed filter... [0.007s] -Searching alignments... [0.324s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.201s] -Building query seed array... [0.098s] -Computing hash join... [0.089s] -Building seed filter... [0.007s] -Searching alignments... [0.248s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.22s] -Building query seed array... [0.111s] -Computing hash join... [0.09s] -Building seed filter... [0.006s] -Searching alignments... [0.243s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.232s] -Building query seed array... [0.11s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.249s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.201s] -Building query seed array... [0.1s] -Computing hash join... [0.088s] -Building seed filter... [0.006s] -Searching alignments... [0.231s] -Deallocating buffers... [0.052s] -Computing alignments... [3.101s] -Deallocating reference... [0.023s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.018s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.126s -Reported 34038 pairwise alignments, 34375 HSPs. -34038 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05/Sr_rh_Bv05_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Bv05_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Bv01.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Bv01.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.556s] -Masking queries... [0.392s] -Building query seed set... [0.047s] -Algorithm: Double-indexed -Building query histograms... [0.126s] -Allocating buffers... [0s] -Loading reference sequences... [1.102s] -Masking reference... [0.703s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.301s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.235s] -Building query seed array... [0.093s] -Computing hash join... [0.113s] -Building seed filter... [0.007s] -Searching alignments... [0.15s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.245s] -Building query seed array... [0.097s] -Computing hash join... [0.097s] -Building seed filter... [0.006s] -Searching alignments... [0.151s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.25s] -Building query seed array... [0.095s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.154s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.212s] -Building query seed array... [0.079s] -Computing hash join... [0.093s] -Building seed filter... [0.006s] -Searching alignments... [0.149s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.217s] -Building query seed array... [0.081s] -Computing hash join... [0.093s] -Building seed filter... [0.006s] -Searching alignments... [0.126s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.238s] -Building query seed array... [0.09s] -Computing hash join... [0.097s] -Building seed filter... [0.006s] -Searching alignments... [0.131s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.248s] -Building query seed array... [0.09s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.131s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.211s] -Building query seed array... [0.082s] -Computing hash join... [0.094s] -Building seed filter... [0.007s] -Searching alignments... [0.129s] -Deallocating buffers... [0.056s] -Computing alignments... [1.438s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.012s] -Deallocating queries... [0.016s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.329s -Reported 17468 pairwise alignments, 17618 HSPs. -17468 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.559s] -Masking queries... [0.421s] -Building query seed set... [0.05s] -Algorithm: Double-indexed -Building query histograms... [0.123s] -Allocating buffers... [0s] -Loading reference sequences... [0.998s] -Masking reference... [0.638s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.275s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.222s] -Building query seed array... [0.099s] -Computing hash join... [0.116s] -Building seed filter... [0.01s] -Searching alignments... [0.318s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.237s] -Building query seed array... [0.097s] -Computing hash join... [0.096s] -Building seed filter... [0.007s] -Searching alignments... [0.276s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.238s] -Building query seed array... [0.099s] -Computing hash join... [0.092s] -Building seed filter... [0.009s] -Searching alignments... [0.286s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.202s] -Building query seed array... [0.086s] -Computing hash join... [0.09s] -Building seed filter... [0.008s] -Searching alignments... [0.309s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.199s] -Building query seed array... [0.077s] -Computing hash join... [0.092s] -Building seed filter... [0.008s] -Searching alignments... [0.244s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.224s] -Building query seed array... [0.086s] -Computing hash join... [0.093s] -Building seed filter... [0.008s] -Searching alignments... [0.207s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.234s] -Building query seed array... [0.093s] -Computing hash join... [0.095s] -Building seed filter... [0.008s] -Searching alignments... [0.204s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.196s] -Building query seed array... [0.08s] -Computing hash join... [0.093s] -Building seed filter... [0.008s] -Searching alignments... [0.204s] -Deallocating buffers... [0.05s] -Computing alignments... [2.675s] -Deallocating reference... [0.022s] -Loading reference sequences... [0s] -Deallocating buffers... [0.012s] -Deallocating queries... [0.016s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 12.237s -Reported 35541 pairwise alignments, 35937 HSPs. -35541 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01/Sr_rh_Bv01_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Bv01_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Slin.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Slin.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.36s] -Masking queries... [0.117s] -Building query seed set... [0.04s] -Algorithm: Double-indexed -Building query histograms... [0.046s] -Allocating buffers... [0s] -Loading reference sequences... [1.089s] -Masking reference... [0.702s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.315s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.232s] -Building query seed array... [0.055s] -Computing hash join... [0.081s] -Building seed filter... [0.004s] -Searching alignments... [0.071s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.246s] -Building query seed array... [0.038s] -Computing hash join... [0.065s] -Building seed filter... [0.005s] -Searching alignments... [0.055s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.253s] -Building query seed array... [0.031s] -Computing hash join... [0.058s] -Building seed filter... [0.005s] -Searching alignments... [0.058s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.208s] -Building query seed array... [0.04s] -Computing hash join... [0.056s] -Building seed filter... [0.004s] -Searching alignments... [0.05s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.224s] -Building query seed array... [0.038s] -Computing hash join... [0.056s] -Building seed filter... [0.004s] -Searching alignments... [0.046s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.233s] -Building query seed array... [0.036s] -Computing hash join... [0.05s] -Building seed filter... [0.004s] -Searching alignments... [0.044s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.248s] -Building query seed array... [0.044s] -Computing hash join... [0.054s] -Building seed filter... [0.004s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.208s] -Building query seed array... [0.038s] -Computing hash join... [0.053s] -Building seed filter... [0.004s] -Searching alignments... [0.044s] -Deallocating buffers... [0.055s] -Computing alignments... [0.446s] -Deallocating reference... [0.025s] -Loading reference sequences... [0s] -Deallocating buffers... [0.003s] -Deallocating queries... [0.005s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 6.344s -Reported 3720 pairwise alignments, 3786 HSPs. -3720 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.379s] -Masking queries... [0.163s] -Building query seed set... [0.041s] -Algorithm: Double-indexed -Building query histograms... [0.046s] -Allocating buffers... [0s] -Loading reference sequences... [0.992s] -Masking reference... [0.639s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.286s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.229s] -Building query seed array... [0.049s] -Computing hash join... [0.074s] -Building seed filter... [0.005s] -Searching alignments... [0.084s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.222s] -Building query seed array... [0.036s] -Computing hash join... [0.054s] -Building seed filter... [0.005s] -Searching alignments... [0.082s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.23s] -Building query seed array... [0.034s] -Computing hash join... [0.052s] -Building seed filter... [0.005s] -Searching alignments... [0.074s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.192s] -Building query seed array... [0.038s] -Computing hash join... [0.05s] -Building seed filter... [0.004s] -Searching alignments... [0.074s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.191s] -Building query seed array... [0.035s] -Computing hash join... [0.05s] -Building seed filter... [0.005s] -Searching alignments... [0.068s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.213s] -Building query seed array... [0.039s] -Computing hash join... [0.05s] -Building seed filter... [0.005s] -Searching alignments... [0.069s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.231s] -Building query seed array... [0.036s] -Computing hash join... [0.05s] -Building seed filter... [0.005s] -Searching alignments... [0.077s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.195s] -Building query seed array... [0.036s] -Computing hash join... [0.051s] -Building seed filter... [0.004s] -Searching alignments... [0.066s] -Deallocating buffers... [0.051s] -Computing alignments... [0.736s] -Deallocating reference... [0.017s] -Loading reference sequences... [0s] -Deallocating buffers... [0.003s] -Deallocating queries... [0.005s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 6.473s -Reported 8131 pairwise alignments, 8278 HSPs. -8131 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin/Sr_rh_Slin_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Slin_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Gl03.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Gl03.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.745s] -Masking queries... [0.498s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.179s] -Allocating buffers... [0s] -Loading reference sequences... [1.084s] -Masking reference... [0.714s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.306s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.233s] -Building query seed array... [0.138s] -Computing hash join... [0.135s] -Building seed filter... [0.011s] -Searching alignments... [0.228s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.248s] -Building query seed array... [0.133s] -Computing hash join... [0.113s] -Building seed filter... [0.009s] -Searching alignments... [0.215s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.254s] -Building query seed array... [0.138s] -Computing hash join... [0.118s] -Building seed filter... [0.009s] -Searching alignments... [0.237s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.229s] -Building query seed array... [0.127s] -Computing hash join... [0.114s] -Building seed filter... [0.008s] -Searching alignments... [0.216s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.208s] -Building query seed array... [0.116s] -Computing hash join... [0.111s] -Building seed filter... [0.008s] -Searching alignments... [0.195s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.244s] -Building query seed array... [0.128s] -Computing hash join... [0.111s] -Building seed filter... [0.009s] -Searching alignments... [0.193s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.245s] -Building query seed array... [0.13s] -Computing hash join... [0.11s] -Building seed filter... [0.009s] -Searching alignments... [0.196s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.114s] -Computing hash join... [0.111s] -Building seed filter... [0.008s] -Searching alignments... [0.191s] -Deallocating buffers... [0.059s] -Computing alignments... [2.383s] -Deallocating reference... [0.023s] -Loading reference sequences... [0s] -Deallocating buffers... [0.022s] -Deallocating queries... [0.022s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 12.681s -Reported 24064 pairwise alignments, 24123 HSPs. -24064 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.762s] -Masking queries... [0.457s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.176s] -Allocating buffers... [0s] -Loading reference sequences... [0.971s] -Masking reference... [0.64s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.287s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.211s] -Building query seed array... [0.128s] -Computing hash join... [0.12s] -Building seed filter... [0.009s] -Searching alignments... [0.31s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.224s] -Building query seed array... [0.127s] -Computing hash join... [0.104s] -Building seed filter... [0.01s] -Searching alignments... [0.308s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.234s] -Building query seed array... [0.133s] -Computing hash join... [0.105s] -Building seed filter... [0.009s] -Searching alignments... [0.287s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.205s] -Building query seed array... [0.116s] -Computing hash join... [0.102s] -Building seed filter... [0.008s] -Searching alignments... [0.288s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.199s] -Building query seed array... [0.12s] -Computing hash join... [0.101s] -Building seed filter... [0.008s] -Searching alignments... [0.253s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.225s] -Building query seed array... [0.129s] -Computing hash join... [0.102s] -Building seed filter... [0.009s] -Searching alignments... [0.246s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.236s] -Building query seed array... [0.145s] -Computing hash join... [0.106s] -Building seed filter... [0.009s] -Searching alignments... [0.249s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.196s] -Building query seed array... [0.116s] -Computing hash join... [0.105s] -Building seed filter... [0.009s] -Searching alignments... [0.242s] -Deallocating buffers... [0.05s] -Computing alignments... [3.854s] -Deallocating reference... [0.024s] -Loading reference sequences... [0s] -Deallocating buffers... [0.022s] -Deallocating queries... [0.022s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 14.194s -Reported 49617 pairwise alignments, 49761 HSPs. -49617 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03/Sr_rh_Gl03_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Gl03_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn09.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn09.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.803s] -Masking queries... [0.454s] -Building query seed set... [0.029s] -Algorithm: Double-indexed -Building query histograms... [0.181s] -Allocating buffers... [0s] -Loading reference sequences... [1.117s] -Masking reference... [1.661s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.319s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.238s] -Building query seed array... [0.132s] -Computing hash join... [0.121s] -Building seed filter... [0.007s] -Searching alignments... [0.188s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.24s] -Building query seed array... [0.136s] -Computing hash join... [0.11s] -Building seed filter... [0.007s] -Searching alignments... [0.178s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.246s] -Building query seed array... [0.134s] -Computing hash join... [0.106s] -Building seed filter... [0.007s] -Searching alignments... [0.178s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.213s] -Building query seed array... [0.119s] -Computing hash join... [0.104s] -Building seed filter... [0.007s] -Searching alignments... [0.187s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.212s] -Building query seed array... [0.116s] -Computing hash join... [0.108s] -Building seed filter... [0.008s] -Searching alignments... [0.165s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.246s] -Building query seed array... [0.135s] -Computing hash join... [0.104s] -Building seed filter... [0.007s] -Searching alignments... [0.166s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.254s] -Building query seed array... [0.135s] -Computing hash join... [0.107s] -Building seed filter... [0.008s] -Searching alignments... [0.16s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.121s] -Computing hash join... [0.106s] -Building seed filter... [0.008s] -Searching alignments... [0.157s] -Deallocating buffers... [0.056s] -Computing alignments... [2.04s] -Deallocating reference... [0.026s] -Loading reference sequences... [0s] -Deallocating buffers... [0.02s] -Deallocating queries... [0.021s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 12.971s -Reported 21847 pairwise alignments, 22013 HSPs. -21847 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.803s] -Masking queries... [0.461s] -Building query seed set... [0.04s] -Algorithm: Double-indexed -Building query histograms... [0.18s] -Allocating buffers... [0s] -Loading reference sequences... [0.989s] -Masking reference... [0.651s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.293s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.22s] -Building query seed array... [0.15s] -Computing hash join... [0.121s] -Building seed filter... [0.008s] -Searching alignments... [0.61s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.23s] -Building query seed array... [0.136s] -Computing hash join... [0.102s] -Building seed filter... [0.008s] -Searching alignments... [0.325s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.134s] -Computing hash join... [0.099s] -Building seed filter... [0.008s] -Searching alignments... [0.414s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.2s] -Building query seed array... [0.116s] -Computing hash join... [0.101s] -Building seed filter... [0.008s] -Searching alignments... [0.615s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.191s] -Building query seed array... [0.12s] -Computing hash join... [0.1s] -Building seed filter... [0.008s] -Searching alignments... [0.442s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.22s] -Building query seed array... [0.131s] -Computing hash join... [0.103s] -Building seed filter... [0.008s] -Searching alignments... [0.429s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.134s] -Computing hash join... [0.099s] -Building seed filter... [0.008s] -Searching alignments... [0.329s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.2s] -Building query seed array... [0.117s] -Computing hash join... [0.099s] -Building seed filter... [0.008s] -Searching alignments... [0.272s] -Deallocating buffers... [0.05s] -Computing alignments... [3.679s] -Deallocating reference... [0.013s] -Loading reference sequences... [0s] -Deallocating buffers... [0.022s] -Deallocating queries... [0.019s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 15.337s -Reported 44982 pairwise alignments, 45503 HSPs. -44982 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09/Sr_rh_Nn09_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn09_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Nn13.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Nn13.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.271s] -Masking queries... [0.345s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.137s] -Allocating buffers... [0s] -Loading reference sequences... [1.096s] -Masking reference... [0.719s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.314s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.234s] -Building query seed array... [0.1s] -Computing hash join... [0.119s] -Building seed filter... [0.008s] -Searching alignments... [0.141s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.235s] -Building query seed array... [0.095s] -Computing hash join... [0.098s] -Building seed filter... [0.008s] -Searching alignments... [0.138s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.249s] -Building query seed array... [0.098s] -Computing hash join... [0.096s] -Building seed filter... [0.006s] -Searching alignments... [0.14s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.232s] -Building query seed array... [0.095s] -Computing hash join... [0.098s] -Building seed filter... [0.006s] -Searching alignments... [0.14s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.21s] -Building query seed array... [0.093s] -Computing hash join... [0.098s] -Building seed filter... [0.007s] -Searching alignments... [0.129s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.241s] -Building query seed array... [0.101s] -Computing hash join... [0.095s] -Building seed filter... [0.006s] -Searching alignments... [0.129s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.259s] -Building query seed array... [0.109s] -Computing hash join... [0.099s] -Building seed filter... [0.007s] -Searching alignments... [0.125s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.21s] -Building query seed array... [0.098s] -Computing hash join... [0.102s] -Building seed filter... [0.007s] -Searching alignments... [0.124s] -Deallocating buffers... [0.058s] -Computing alignments... [1.314s] -Deallocating reference... [0.018s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.013s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 9.969s -Reported 13752 pairwise alignments, 13820 HSPs. -13752 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.274s] -Masking queries... [0.342s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.147s] -Allocating buffers... [0s] -Loading reference sequences... [0.985s] -Masking reference... [0.639s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.287s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.219s] -Building query seed array... [0.101s] -Computing hash join... [0.099s] -Building seed filter... [0.006s] -Searching alignments... [0.36s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.221s] -Building query seed array... [0.1s] -Computing hash join... [0.09s] -Building seed filter... [0.007s] -Searching alignments... [0.286s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.101s] -Computing hash join... [0.091s] -Building seed filter... [0.007s] -Searching alignments... [0.244s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.198s] -Building query seed array... [0.091s] -Computing hash join... [0.093s] -Building seed filter... [0.007s] -Searching alignments... [0.312s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.201s] -Building query seed array... [0.089s] -Computing hash join... [0.091s] -Building seed filter... [0.007s] -Searching alignments... [0.189s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.227s] -Building query seed array... [0.103s] -Computing hash join... [0.091s] -Building seed filter... [0.008s] -Searching alignments... [0.191s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.233s] -Building query seed array... [0.101s] -Computing hash join... [0.089s] -Building seed filter... [0.007s] -Searching alignments... [0.19s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.194s] -Building query seed array... [0.089s] -Computing hash join... [0.091s] -Building seed filter... [0.007s] -Searching alignments... [0.182s] -Deallocating buffers... [0.052s] -Computing alignments... [2.506s] -Deallocating reference... [0.016s] -Loading reference sequences... [0s] -Deallocating buffers... [0.016s] -Deallocating queries... [0.014s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 11.607s -Reported 29317 pairwise alignments, 29537 HSPs. -29317 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13/Sr_rh_Nn13_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Nn13_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -Warning: [blastn] Examining 5 or more matches is recommended - - -BLASTing Sr_rh_Atps.200bp.fasta against the rDNA database - - -Binning Sequences from Sr_rh_Atps.200bp.fasta -as rDNA OR Potentially Protein-Coding - - - -Look for beegfs_NorRNAseqs.fasta -in the beegfs Folder - - -Next Script is: 2b_remove_Bact.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/micout.dmnd -Sequences = 1451565 -Letters = 458122721 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.145s] -Masking queries... [0.066s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.033s] -Allocating buffers... [0s] -Loading reference sequences... [1.088s] -Masking reference... [0.689s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.316s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.229s] -Building query seed array... [0.034s] -Computing hash join... [0.059s] -Building seed filter... [0.004s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.245s] -Building query seed array... [0.03s] -Computing hash join... [0.044s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.259s] -Building query seed array... [0.029s] -Computing hash join... [0.04s] -Building seed filter... [0.004s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.207s] -Building query seed array... [0.023s] -Computing hash join... [0.042s] -Building seed filter... [0.004s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.207s] -Building query seed array... [0.022s] -Computing hash join... [0.039s] -Building seed filter... [0.004s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.24s] -Building query seed array... [0.028s] -Computing hash join... [0.038s] -Building seed filter... [0.004s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.242s] -Building query seed array... [0.023s] -Computing hash join... [0.038s] -Building seed filter... [0.004s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.203s] -Building query seed array... [0.02s] -Computing hash join... [0.039s] -Building seed filter... [0.004s] -Searching alignments... [0.026s] -Deallocating buffers... [0.055s] -Computing alignments... [0.218s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0.002s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 5.342s -Reported 2739 pairwise alignments, 2882 HSPs. -2739 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps/BvE -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_BvsE/eukout.dmnd -Sequences = 884771 -Letters = 428734159 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.153s] -Masking queries... [0.058s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.032s] -Allocating buffers... [0s] -Loading reference sequences... [0.988s] -Masking reference... [0.639s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.282s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.221s] -Building query seed array... [0.028s] -Computing hash join... [0.039s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.223s] -Building query seed array... [0.028s] -Computing hash join... [0.034s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.22s] -Building query seed array... [0.026s] -Computing hash join... [0.035s] -Building seed filter... [0.004s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.189s] -Building query seed array... [0.024s] -Computing hash join... [0.034s] -Building seed filter... [0.004s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.191s] -Building query seed array... [0.027s] -Computing hash join... [0.037s] -Building seed filter... [0.004s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.212s] -Building query seed array... [0.023s] -Computing hash join... [0.034s] -Building seed filter... [0.004s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.226s] -Building query seed array... [0.025s] -Computing hash join... [0.034s] -Building seed filter... [0.004s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.191s] -Building query seed array... [0.027s] -Computing hash join... [0.035s] -Building seed filter... [0.004s] -Searching alignments... [0.027s] -Deallocating buffers... [0.052s] -Computing alignments... [0.125s] -Deallocating reference... [0.023s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0.002s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 4.805s -Reported 1289 pairwise alignments, 1382 HSPs. -1289 queries aligned. -/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps/Sr_rh_Atps_NorRNAseqs.fasta - - -"BLAST"-ing against PROK database using DIAMOND: micout.dmnd - - - - -"BLAST"-ing against EUK database using DIAMOND: eukout.dmnd - - - -Look for Sr_rh_Atps_WTA_EPU.fasta in the beegfs Folder - - -Next Script is: 3_CountOGsDiamond.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.223s] -Masking queries... [0.467s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.145s] -Allocating buffers... [0s] -Loading reference sequences... [1.597s] -Masking reference... [1.189s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.447s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.345s] -Building query seed array... [0.103s] -Computing hash join... [0.14s] -Building seed filter... [0.008s] -Searching alignments... [0.396s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.38s] -Building query seed array... [0.099s] -Computing hash join... [0.128s] -Building seed filter... [0.009s] -Searching alignments... [0.39s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.375s] -Building query seed array... [0.102s] -Computing hash join... [0.128s] -Building seed filter... [0.009s] -Searching alignments... [0.36s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.323s] -Building query seed array... [0.086s] -Computing hash join... [0.124s] -Building seed filter... [0.009s] -Searching alignments... [0.364s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.319s] -Building query seed array... [0.091s] -Computing hash join... [0.128s] -Building seed filter... [0.011s] -Searching alignments... [0.325s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.374s] -Building query seed array... [0.102s] -Computing hash join... [0.124s] -Building seed filter... [0.008s] -Searching alignments... [0.31s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.096s] -Computing hash join... [0.13s] -Building seed filter... [0.009s] -Searching alignments... [0.332s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.314s] -Building query seed array... [0.086s] -Computing hash join... [0.124s] -Building seed filter... [0.008s] -Searching alignments... [0.312s] -Deallocating buffers... [0.093s] -Computing alignments... [7.27s] -Deallocating reference... [0.034s] -Loading reference sequences... [0s] -Deallocating buffers... [0.013s] -Deallocating queries... [0.016s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 20.043s -Reported 354463 pairwise alignments, 356676 HSPs. -18186 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn02_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.297s] -Masking queries... [0.103s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.046s] -Allocating buffers... [0s] -Loading reference sequences... [1.611s] -Masking reference... [1.323s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.457s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.356s] -Building query seed array... [0.054s] -Computing hash join... [0.119s] -Building seed filter... [0.005s] -Searching alignments... [0.122s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.366s] -Building query seed array... [0.038s] -Computing hash join... [0.088s] -Building seed filter... [0.005s] -Searching alignments... [0.114s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.045s] -Computing hash join... [0.087s] -Building seed filter... [0.006s] -Searching alignments... [0.117s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.32s] -Building query seed array... [0.035s] -Computing hash join... [0.086s] -Building seed filter... [0.005s] -Searching alignments... [0.109s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.314s] -Building query seed array... [0.037s] -Computing hash join... [0.081s] -Building seed filter... [0.005s] -Searching alignments... [0.105s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.357s] -Building query seed array... [0.033s] -Computing hash join... [0.084s] -Building seed filter... [0.005s] -Searching alignments... [0.099s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.372s] -Building query seed array... [0.038s] -Computing hash join... [0.083s] -Building seed filter... [0.005s] -Searching alignments... [0.1s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.309s] -Building query seed array... [0.036s] -Computing hash join... [0.082s] -Building seed filter... [0.005s] -Searching alignments... [0.097s] -Deallocating buffers... [0.094s] -Computing alignments... [3.364s] -Deallocating reference... [0.036s] -Loading reference sequences... [0s] -Deallocating buffers... [0.002s] -Deallocating queries... [0.003s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 12.124s -Reported 141326 pairwise alignments, 143069 HSPs. -7105 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Gspa_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.256s] -Masking queries... [0.342s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.132s] -Allocating buffers... [0s] -Loading reference sequences... [1.602s] -Masking reference... [1.062s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.466s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.349s] -Building query seed array... [0.104s] -Computing hash join... [0.142s] -Building seed filter... [0.008s] -Searching alignments... [0.431s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.369s] -Building query seed array... [0.103s] -Computing hash join... [0.131s] -Building seed filter... [0.009s] -Searching alignments... [0.4s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.382s] -Building query seed array... [0.109s] -Computing hash join... [0.131s] -Building seed filter... [0.009s] -Searching alignments... [0.369s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.095s] -Computing hash join... [0.13s] -Building seed filter... [0.009s] -Searching alignments... [0.357s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.321s] -Building query seed array... [0.095s] -Computing hash join... [0.127s] -Building seed filter... [0.009s] -Searching alignments... [0.377s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.368s] -Building query seed array... [0.104s] -Computing hash join... [0.125s] -Building seed filter... [0.008s] -Searching alignments... [0.342s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.375s] -Building query seed array... [0.101s] -Computing hash join... [0.125s] -Building seed filter... [0.009s] -Searching alignments... [0.375s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.339s] -Building query seed array... [0.092s] -Computing hash join... [0.125s] -Building seed filter... [0.011s] -Searching alignments... [0.28s] -Deallocating buffers... [0.096s] -Computing alignments... [7.307s] -Deallocating reference... [0.035s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.017s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 20.076s -Reported 384072 pairwise alignments, 385929 HSPs. -19812 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn06_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.862s] -Masking queries... [0.491s] -Building query seed set... [0.05s] -Algorithm: Double-indexed -Building query histograms... [0.163s] -Allocating buffers... [0s] -Loading reference sequences... [1.588s] -Masking reference... [1.043s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.442s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.343s] -Building query seed array... [0.117s] -Computing hash join... [0.146s] -Building seed filter... [0.009s] -Searching alignments... [0.495s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.107s] -Computing hash join... [0.13s] -Building seed filter... [0.01s] -Searching alignments... [0.448s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.393s] -Building query seed array... [0.123s] -Computing hash join... [0.127s] -Building seed filter... [0.01s] -Searching alignments... [0.399s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.327s] -Building query seed array... [0.109s] -Computing hash join... [0.13s] -Building seed filter... [0.009s] -Searching alignments... [0.403s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.314s] -Building query seed array... [0.1s] -Computing hash join... [0.133s] -Building seed filter... [0.01s] -Searching alignments... [0.386s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.111s] -Computing hash join... [0.121s] -Building seed filter... [0.011s] -Searching alignments... [0.354s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.374s] -Building query seed array... [0.119s] -Computing hash join... [0.131s] -Building seed filter... [0.011s] -Searching alignments... [0.369s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.099s] -Computing hash join... [0.129s] -Building seed filter... [0.012s] -Searching alignments... [0.33s] -Deallocating buffers... [0.096s] -Computing alignments... [8.467s] -Deallocating reference... [0.035s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.026s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 22.321s -Reported 464168 pairwise alignments, 469292 HSPs. -24278 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Bv02_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.871s] -Masking queries... [0.256s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.104s] -Allocating buffers... [0s] -Loading reference sequences... [1.572s] -Masking reference... [1.051s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.473s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.348s] -Building query seed array... [0.083s] -Computing hash join... [0.161s] -Building seed filter... [0.008s] -Searching alignments... [0.223s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.365s] -Building query seed array... [0.093s] -Computing hash join... [0.126s] -Building seed filter... [0.007s] -Searching alignments... [0.208s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.397s] -Building query seed array... [0.077s] -Computing hash join... [0.122s] -Building seed filter... [0.008s] -Searching alignments... [0.206s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.074s] -Computing hash join... [0.123s] -Building seed filter... [0.007s] -Searching alignments... [0.199s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.313s] -Building query seed array... [0.073s] -Computing hash join... [0.122s] -Building seed filter... [0.008s] -Searching alignments... [0.177s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.081s] -Computing hash join... [0.123s] -Building seed filter... [0.008s] -Searching alignments... [0.183s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.378s] -Building query seed array... [0.082s] -Computing hash join... [0.123s] -Building seed filter... [0.008s] -Searching alignments... [0.177s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.074s] -Computing hash join... [0.123s] -Building seed filter... [0.008s] -Searching alignments... [0.183s] -Deallocating buffers... [0.095s] -Computing alignments... [5.504s] -Deallocating reference... [0.035s] -Loading reference sequences... [0s] -Deallocating buffers... [0.012s] -Deallocating queries... [0.014s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 16.157s -Reported 220479 pairwise alignments, 220717 HSPs. -10997 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Hind_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.123s] -Masking queries... [0.311s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.119s] -Allocating buffers... [0s] -Loading reference sequences... [1.577s] -Masking reference... [1.058s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.463s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.337s] -Building query seed array... [0.083s] -Computing hash join... [0.19s] -Building seed filter... [0.009s] -Searching alignments... [0.295s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.365s] -Building query seed array... [0.086s] -Computing hash join... [0.128s] -Building seed filter... [0.009s] -Searching alignments... [0.279s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.376s] -Building query seed array... [0.089s] -Computing hash join... [0.129s] -Building seed filter... [0.009s] -Searching alignments... [0.261s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.082s] -Computing hash join... [0.13s] -Building seed filter... [0.009s] -Searching alignments... [0.258s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.317s] -Building query seed array... [0.079s] -Computing hash join... [0.132s] -Building seed filter... [0.009s] -Searching alignments... [0.237s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.358s] -Building query seed array... [0.086s] -Computing hash join... [0.132s] -Building seed filter... [0.01s] -Searching alignments... [0.24s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.374s] -Building query seed array... [0.095s] -Computing hash join... [0.137s] -Building seed filter... [0.01s] -Searching alignments... [0.234s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.077s] -Computing hash join... [0.129s] -Building seed filter... [0.01s] -Searching alignments... [0.226s] -Deallocating buffers... [0.094s] -Computing alignments... [5.707s] -Deallocating reference... [0.021s] -Loading reference sequences... [0s] -Deallocating buffers... [0.012s] -Deallocating queries... [0.012s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 17.227s -Reported 312594 pairwise alignments, 314266 HSPs. -16742 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn11_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.782s] -Masking queries... [0.507s] -Building query seed set... [0.052s] -Algorithm: Double-indexed -Building query histograms... [0.147s] -Allocating buffers... [0s] -Loading reference sequences... [1.609s] -Masking reference... [1.153s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.451s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.348s] -Building query seed array... [0.105s] -Computing hash join... [0.188s] -Building seed filter... [0.01s] -Searching alignments... [0.432s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.374s] -Building query seed array... [0.105s] -Computing hash join... [0.125s] -Building seed filter... [0.01s] -Searching alignments... [0.387s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.376s] -Building query seed array... [0.113s] -Computing hash join... [0.13s] -Building seed filter... [0.012s] -Searching alignments... [0.375s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.099s] -Computing hash join... [0.128s] -Building seed filter... [0.011s] -Searching alignments... [0.38s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.317s] -Building query seed array... [0.092s] -Computing hash join... [0.129s] -Building seed filter... [0.009s] -Searching alignments... [0.357s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.365s] -Building query seed array... [0.105s] -Computing hash join... [0.128s] -Building seed filter... [0.009s] -Searching alignments... [0.342s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.377s] -Building query seed array... [0.113s] -Computing hash join... [0.129s] -Building seed filter... [0.009s] -Searching alignments... [0.354s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.092s] -Computing hash join... [0.126s] -Building seed filter... [0.009s] -Searching alignments... [0.333s] -Deallocating buffers... [0.093s] -Computing alignments... [8.04s] -Deallocating reference... [0.036s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.025s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 21.697s -Reported 442574 pairwise alignments, 448696 HSPs. -23147 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Bv03_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.595s] -Masking queries... [0.192s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.071s] -Allocating buffers... [0s] -Loading reference sequences... [1.591s] -Masking reference... [1.117s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.475s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.355s] -Building query seed array... [0.062s] -Computing hash join... [0.156s] -Building seed filter... [0.006s] -Searching alignments... [0.175s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.06s] -Computing hash join... [0.126s] -Building seed filter... [0.007s] -Searching alignments... [0.169s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.059s] -Computing hash join... [0.123s] -Building seed filter... [0.006s] -Searching alignments... [0.157s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.314s] -Building query seed array... [0.051s] -Computing hash join... [0.121s] -Building seed filter... [0.007s] -Searching alignments... [0.156s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.325s] -Building query seed array... [0.053s] -Computing hash join... [0.111s] -Building seed filter... [0.007s] -Searching alignments... [0.14s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.359s] -Building query seed array... [0.055s] -Computing hash join... [0.111s] -Building seed filter... [0.007s] -Searching alignments... [0.145s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.387s] -Building query seed array... [0.062s] -Computing hash join... [0.116s] -Building seed filter... [0.007s] -Searching alignments... [0.143s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.311s] -Building query seed array... [0.052s] -Computing hash join... [0.118s] -Building seed filter... [0.007s] -Searching alignments... [0.137s] -Deallocating buffers... [0.094s] -Computing alignments... [3.907s] -Deallocating reference... [0.037s] -Loading reference sequences... [0s] -Deallocating buffers... [0.006s] -Deallocating queries... [0.011s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.69s -Reported 174844 pairwise alignments, 175037 HSPs. -9075 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Gsp1_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.979s] -Masking queries... [0.266s] -Building query seed set... [0.044s] -Algorithm: Double-indexed -Building query histograms... [0.09s] -Allocating buffers... [0s] -Loading reference sequences... [1.6s] -Masking reference... [1.105s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.466s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.334s] -Building query seed array... [0.072s] -Computing hash join... [0.199s] -Building seed filter... [0.012s] -Searching alignments... [0.239s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.373s] -Building query seed array... [0.067s] -Computing hash join... [0.136s] -Building seed filter... [0.006s] -Searching alignments... [0.217s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.398s] -Building query seed array... [0.067s] -Computing hash join... [0.129s] -Building seed filter... [0.006s] -Searching alignments... [0.203s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.318s] -Building query seed array... [0.061s] -Computing hash join... [0.127s] -Building seed filter... [0.006s] -Searching alignments... [0.218s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.315s] -Building query seed array... [0.057s] -Computing hash join... [0.124s] -Building seed filter... [0.006s] -Searching alignments... [0.199s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.368s] -Building query seed array... [0.067s] -Computing hash join... [0.125s] -Building seed filter... [0.006s] -Searching alignments... [0.186s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.381s] -Building query seed array... [0.067s] -Computing hash join... [0.121s] -Building seed filter... [0.006s] -Searching alignments... [0.192s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.314s] -Building query seed array... [0.053s] -Computing hash join... [0.123s] -Building seed filter... [0.006s] -Searching alignments... [0.183s] -Deallocating buffers... [0.094s] -Computing alignments... [4.041s] -Deallocating reference... [0.031s] -Loading reference sequences... [0s] -Deallocating buffers... [0.006s] -Deallocating queries... [0.009s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 14.867s -Reported 250746 pairwise alignments, 252735 HSPs. -13330 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Bv06_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.044s] -Masking queries... [0.068s] -Building query seed set... [0.031s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [1.589s] -Masking reference... [1.063s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.447s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.352s] -Building query seed array... [0.009s] -Computing hash join... [0.079s] -Building seed filter... [0.005s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.356s] -Building query seed array... [0.007s] -Computing hash join... [0.075s] -Building seed filter... [0.004s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.37s] -Building query seed array... [0.007s] -Computing hash join... [0.076s] -Building seed filter... [0.005s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.009s] -Computing hash join... [0.077s] -Building seed filter... [0.004s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.316s] -Building query seed array... [0.01s] -Computing hash join... [0.079s] -Building seed filter... [0.004s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.362s] -Building query seed array... [0.009s] -Computing hash join... [0.076s] -Building seed filter... [0.004s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.373s] -Building query seed array... [0.009s] -Computing hash join... [0.079s] -Building seed filter... [0.004s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.323s] -Building query seed array... [0.014s] -Computing hash join... [0.081s] -Building seed filter... [0.004s] -Searching alignments... [0.035s] -Deallocating buffers... [0.098s] -Computing alignments... [0.344s] -Deallocating reference... [0.03s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 7.513s -Reported 25154 pairwise alignments, 25213 HSPs. -1224 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Gl01_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.713s] -Masking queries... [0.209s] -Building query seed set... [0.043s] -Algorithm: Double-indexed -Building query histograms... [0.075s] -Allocating buffers... [0s] -Loading reference sequences... [1.588s] -Masking reference... [1.044s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.447s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.341s] -Building query seed array... [0.061s] -Computing hash join... [0.15s] -Building seed filter... [0.008s] -Searching alignments... [0.204s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.365s] -Building query seed array... [0.056s] -Computing hash join... [0.122s] -Building seed filter... [0.008s] -Searching alignments... [0.187s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.383s] -Building query seed array... [0.062s] -Computing hash join... [0.113s] -Building seed filter... [0.007s] -Searching alignments... [0.175s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.314s] -Building query seed array... [0.053s] -Computing hash join... [0.111s] -Building seed filter... [0.008s] -Searching alignments... [0.181s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.324s] -Building query seed array... [0.056s] -Computing hash join... [0.107s] -Building seed filter... [0.007s] -Searching alignments... [0.169s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.06s] -Computing hash join... [0.11s] -Building seed filter... [0.007s] -Searching alignments... [0.159s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.381s] -Building query seed array... [0.056s] -Computing hash join... [0.107s] -Building seed filter... [0.007s] -Searching alignments... [0.164s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.317s] -Building query seed array... [0.049s] -Computing hash join... [0.105s] -Building seed filter... [0.007s] -Searching alignments... [0.154s] -Deallocating buffers... [0.095s] -Computing alignments... [3.829s] -Deallocating reference... [0.029s] -Loading reference sequences... [0s] -Deallocating buffers... [0.006s] -Deallocating queries... [0.013s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.753s -Reported 211705 pairwise alignments, 212271 HSPs. -11092 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Esca_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.785s] -Masking queries... [0.213s] -Building query seed set... [0.041s] -Algorithm: Double-indexed -Building query histograms... [0.086s] -Allocating buffers... [0s] -Loading reference sequences... [1.587s] -Masking reference... [1.104s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.447s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.339s] -Building query seed array... [0.057s] -Computing hash join... [0.175s] -Building seed filter... [0.007s] -Searching alignments... [0.205s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.369s] -Building query seed array... [0.062s] -Computing hash join... [0.141s] -Building seed filter... [0.009s] -Searching alignments... [0.187s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.382s] -Building query seed array... [0.062s] -Computing hash join... [0.137s] -Building seed filter... [0.008s] -Searching alignments... [0.175s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.058s] -Computing hash join... [0.129s] -Building seed filter... [0.007s] -Searching alignments... [0.175s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.312s] -Building query seed array... [0.059s] -Computing hash join... [0.135s] -Building seed filter... [0.007s] -Searching alignments... [0.162s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.358s] -Building query seed array... [0.07s] -Computing hash join... [0.132s] -Building seed filter... [0.007s] -Searching alignments... [0.178s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.07s] -Computing hash join... [0.128s] -Building seed filter... [0.008s] -Searching alignments... [0.161s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.318s] -Building query seed array... [0.054s] -Computing hash join... [0.127s] -Building seed filter... [0.007s] -Searching alignments... [0.155s] -Deallocating buffers... [0.097s] -Computing alignments... [4.221s] -Deallocating reference... [0.031s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.01s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 14.503s -Reported 205337 pairwise alignments, 206188 HSPs. -10532 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Calb_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.728s] -Masking queries... [0.252s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.088s] -Allocating buffers... [0s] -Loading reference sequences... [1.582s] -Masking reference... [1.099s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.488s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.341s] -Building query seed array... [0.082s] -Computing hash join... [0.19s] -Building seed filter... [0.005s] -Searching alignments... [0.184s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.365s] -Building query seed array... [0.066s] -Computing hash join... [0.148s] -Building seed filter... [0.006s] -Searching alignments... [0.177s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.381s] -Building query seed array... [0.071s] -Computing hash join... [0.143s] -Building seed filter... [0.006s] -Searching alignments... [0.171s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.317s] -Building query seed array... [0.067s] -Computing hash join... [0.142s] -Building seed filter... [0.006s] -Searching alignments... [0.169s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.319s] -Building query seed array... [0.061s] -Computing hash join... [0.137s] -Building seed filter... [0.008s] -Searching alignments... [0.159s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.367s] -Building query seed array... [0.082s] -Computing hash join... [0.14s] -Building seed filter... [0.008s] -Searching alignments... [0.161s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.374s] -Building query seed array... [0.081s] -Computing hash join... [0.139s] -Building seed filter... [0.008s] -Searching alignments... [0.154s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.064s] -Computing hash join... [0.137s] -Building seed filter... [0.008s] -Searching alignments... [0.152s] -Deallocating buffers... [0.094s] -Computing alignments... [3.98s] -Deallocating reference... [0.034s] -Loading reference sequences... [0s] -Deallocating buffers... [0.009s] -Deallocating queries... [0.01s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 14.357s -Reported 186068 pairwise alignments, 186401 HSPs. -9237 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Emac_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.138s] -Masking queries... [0.3s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.114s] -Allocating buffers... [0s] -Loading reference sequences... [1.623s] -Masking reference... [1.064s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.476s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.352s] -Building query seed array... [0.082s] -Computing hash join... [0.153s] -Building seed filter... [0.009s] -Searching alignments... [0.389s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.364s] -Building query seed array... [0.091s] -Computing hash join... [0.129s] -Building seed filter... [0.009s] -Searching alignments... [0.289s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.089s] -Computing hash join... [0.131s] -Building seed filter... [0.011s] -Searching alignments... [0.326s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.323s] -Building query seed array... [0.083s] -Computing hash join... [0.134s] -Building seed filter... [0.01s] -Searching alignments... [0.317s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.315s] -Building query seed array... [0.081s] -Computing hash join... [0.131s] -Building seed filter... [0.009s] -Searching alignments... [0.251s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.088s] -Computing hash join... [0.13s] -Building seed filter... [0.008s] -Searching alignments... [0.257s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.376s] -Building query seed array... [0.091s] -Computing hash join... [0.13s] -Building seed filter... [0.01s] -Searching alignments... [0.328s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.324s] -Building query seed array... [0.086s] -Computing hash join... [0.131s] -Building seed filter... [0.009s] -Searching alignments... [0.238s] -Deallocating buffers... [0.095s] -Computing alignments... [6.416s] -Deallocating reference... [0.037s] -Loading reference sequences... [0s] -Deallocating buffers... [0.013s] -Deallocating queries... [0.017s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 18.401s -Reported 332050 pairwise alignments, 333483 HSPs. -17028 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn05_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.339s] -Masking queries... [0.361s] -Building query seed set... [0.041s] -Algorithm: Double-indexed -Building query histograms... [0.165s] -Allocating buffers... [0s] -Loading reference sequences... [1.602s] -Masking reference... [1.146s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.453s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.336s] -Building query seed array... [0.121s] -Computing hash join... [0.15s] -Building seed filter... [0.012s] -Searching alignments... [0.506s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.109s] -Computing hash join... [0.128s] -Building seed filter... [0.012s] -Searching alignments... [0.461s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.106s] -Computing hash join... [0.129s] -Building seed filter... [0.01s] -Searching alignments... [0.419s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.098s] -Computing hash join... [0.134s] -Building seed filter... [0.011s] -Searching alignments... [0.4s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.315s] -Building query seed array... [0.103s] -Computing hash join... [0.128s] -Building seed filter... [0.009s] -Searching alignments... [0.389s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.362s] -Building query seed array... [0.107s] -Computing hash join... [0.131s] -Building seed filter... [0.01s] -Searching alignments... [0.354s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.387s] -Building query seed array... [0.11s] -Computing hash join... [0.132s] -Building seed filter... [0.01s] -Searching alignments... [0.398s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.098s] -Computing hash join... [0.131s] -Building seed filter... [0.009s] -Searching alignments... [0.304s] -Deallocating buffers... [0.096s] -Computing alignments... [8.481s] -Deallocating reference... [0.037s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.017s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 21.804s -Reported 396857 pairwise alignments, 399100 HSPs. -20167 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn10_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.203s] -Masking queries... [0.377s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.12s] -Allocating buffers... [0s] -Loading reference sequences... [1.61s] -Masking reference... [1.157s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.439s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.341s] -Building query seed array... [0.099s] -Computing hash join... [0.152s] -Building seed filter... [0.011s] -Searching alignments... [0.38s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.364s] -Building query seed array... [0.093s] -Computing hash join... [0.128s] -Building seed filter... [0.01s] -Searching alignments... [0.355s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.386s] -Building query seed array... [0.105s] -Computing hash join... [0.131s] -Building seed filter... [0.011s] -Searching alignments... [0.323s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.081s] -Computing hash join... [0.131s] -Building seed filter... [0.009s] -Searching alignments... [0.338s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.32s] -Building query seed array... [0.087s] -Computing hash join... [0.127s] -Building seed filter... [0.01s] -Searching alignments... [0.307s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.367s] -Building query seed array... [0.092s] -Computing hash join... [0.127s] -Building seed filter... [0.008s] -Searching alignments... [0.29s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.381s] -Building query seed array... [0.1s] -Computing hash join... [0.129s] -Building seed filter... [0.008s] -Searching alignments... [0.337s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.314s] -Building query seed array... [0.089s] -Computing hash join... [0.124s] -Building seed filter... [0.008s] -Searching alignments... [0.287s] -Deallocating buffers... [0.093s] -Computing alignments... [7.075s] -Deallocating reference... [0.039s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.016s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 19.506s -Reported 345493 pairwise alignments, 348050 HSPs. -17953 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn03_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.188s] -Masking queries... [0.38s] -Building query seed set... [0.065s] -Algorithm: Double-indexed -Building query histograms... [0.151s] -Allocating buffers... [0s] -Loading reference sequences... [1.613s] -Masking reference... [1.123s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.474s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.342s] -Building query seed array... [0.102s] -Computing hash join... [0.143s] -Building seed filter... [0.008s] -Searching alignments... [0.298s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.362s] -Building query seed array... [0.104s] -Computing hash join... [0.122s] -Building seed filter... [0.007s] -Searching alignments... [0.312s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.105s] -Computing hash join... [0.123s] -Building seed filter... [0.007s] -Searching alignments... [0.272s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.317s] -Building query seed array... [0.095s] -Computing hash join... [0.128s] -Building seed filter... [0.007s] -Searching alignments... [0.279s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.326s] -Building query seed array... [0.095s] -Computing hash join... [0.122s] -Building seed filter... [0.006s] -Searching alignments... [0.241s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.359s] -Building query seed array... [0.099s] -Computing hash join... [0.122s] -Building seed filter... [0.006s] -Searching alignments... [0.244s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.375s] -Building query seed array... [0.11s] -Computing hash join... [0.126s] -Building seed filter... [0.008s] -Searching alignments... [0.26s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.325s] -Building query seed array... [0.096s] -Computing hash join... [0.124s] -Building seed filter... [0.006s] -Searching alignments... [0.232s] -Deallocating buffers... [0.094s] -Computing alignments... [7.456s] -Deallocating reference... [0.035s] -Loading reference sequences... [0s] -Deallocating buffers... [0.016s] -Deallocating queries... [0.018s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 19.458s -Reported 300277 pairwise alignments, 300581 HSPs. -14869 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Halb_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.083s] -Masking queries... [0.305s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.115s] -Allocating buffers... [0s] -Loading reference sequences... [1.605s] -Masking reference... [1.057s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.494s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.341s] -Building query seed array... [0.094s] -Computing hash join... [0.164s] -Building seed filter... [0.008s] -Searching alignments... [0.39s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.367s] -Building query seed array... [0.079s] -Computing hash join... [0.133s] -Building seed filter... [0.009s] -Searching alignments... [0.362s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.377s] -Building query seed array... [0.082s] -Computing hash join... [0.135s] -Building seed filter... [0.009s] -Searching alignments... [0.325s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.317s] -Building query seed array... [0.077s] -Computing hash join... [0.134s] -Building seed filter... [0.008s] -Searching alignments... [0.329s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.326s] -Building query seed array... [0.073s] -Computing hash join... [0.132s] -Building seed filter... [0.008s] -Searching alignments... [0.333s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.38s] -Building query seed array... [0.082s] -Computing hash join... [0.131s] -Building seed filter... [0.008s] -Searching alignments... [0.28s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.381s] -Building query seed array... [0.094s] -Computing hash join... [0.135s] -Building seed filter... [0.008s] -Searching alignments... [0.346s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.072s] -Computing hash join... [0.132s] -Building seed filter... [0.008s] -Searching alignments... [0.294s] -Deallocating buffers... [0.094s] -Computing alignments... [5.809s] -Deallocating reference... [0.036s] -Loading reference sequences... [0s] -Deallocating buffers... [0.012s] -Deallocating queries... [0.016s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 17.987s -Reported 309767 pairwise alignments, 311870 HSPs. -15500 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn08_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.412s] -Masking queries... [0.368s] -Building query seed set... [0.056s] -Algorithm: Double-indexed -Building query histograms... [0.131s] -Allocating buffers... [0s] -Loading reference sequences... [1.596s] -Masking reference... [1.06s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.463s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.339s] -Building query seed array... [0.107s] -Computing hash join... [0.139s] -Building seed filter... [0.007s] -Searching alignments... [0.383s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.362s] -Building query seed array... [0.107s] -Computing hash join... [0.112s] -Building seed filter... [0.009s] -Searching alignments... [0.346s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.378s] -Building query seed array... [0.093s] -Computing hash join... [0.118s] -Building seed filter... [0.009s] -Searching alignments... [0.316s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.083s] -Computing hash join... [0.109s] -Building seed filter... [0.009s] -Searching alignments... [0.318s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.321s] -Building query seed array... [0.09s] -Computing hash join... [0.114s] -Building seed filter... [0.007s] -Searching alignments... [0.29s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.361s] -Building query seed array... [0.098s] -Computing hash join... [0.111s] -Building seed filter... [0.007s] -Searching alignments... [0.28s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.385s] -Building query seed array... [0.102s] -Computing hash join... [0.11s] -Building seed filter... [0.007s] -Searching alignments... [0.296s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.313s] -Building query seed array... [0.084s] -Computing hash join... [0.112s] -Building seed filter... [0.008s] -Searching alignments... [0.265s] -Deallocating buffers... [0.094s] -Computing alignments... [9.117s] -Deallocating reference... [0.034s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.016s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 21.434s -Reported 403699 pairwise alignments, 404113 HSPs. -19985 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Tx01_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.575s] -Masking queries... [0.392s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.149s] -Allocating buffers... [0s] -Loading reference sequences... [1.587s] -Masking reference... [1.043s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.486s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.346s] -Building query seed array... [0.12s] -Computing hash join... [0.15s] -Building seed filter... [0.014s] -Searching alignments... [0.527s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.37s] -Building query seed array... [0.115s] -Computing hash join... [0.135s] -Building seed filter... [0.013s] -Searching alignments... [0.479s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.38s] -Building query seed array... [0.12s] -Computing hash join... [0.134s] -Building seed filter... [0.012s] -Searching alignments... [0.431s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.331s] -Building query seed array... [0.101s] -Computing hash join... [0.128s] -Building seed filter... [0.014s] -Searching alignments... [0.417s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.317s] -Building query seed array... [0.107s] -Computing hash join... [0.131s] -Building seed filter... [0.01s] -Searching alignments... [0.406s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.364s] -Building query seed array... [0.114s] -Computing hash join... [0.134s] -Building seed filter... [0.01s] -Searching alignments... [0.365s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.383s] -Building query seed array... [0.123s] -Computing hash join... [0.132s] -Building seed filter... [0.01s] -Searching alignments... [0.425s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.318s] -Building query seed array... [0.106s] -Computing hash join... [0.135s] -Building seed filter... [0.011s] -Searching alignments... [0.36s] -Deallocating buffers... [0.092s] -Computing alignments... [8.807s] -Deallocating reference... [0.035s] -Loading reference sequences... [0s] -Deallocating buffers... [0.017s] -Deallocating queries... [0.021s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 22.588s -Reported 468908 pairwise alignments, 470976 HSPs. -23977 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn07_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.342s] -Masking queries... [0.383s] -Building query seed set... [0.042s] -Algorithm: Double-indexed -Building query histograms... [0.146s] -Allocating buffers... [0s] -Loading reference sequences... [1.591s] -Masking reference... [1.057s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.44s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.343s] -Building query seed array... [0.115s] -Computing hash join... [0.144s] -Building seed filter... [0.009s] -Searching alignments... [0.49s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.367s] -Building query seed array... [0.102s] -Computing hash join... [0.132s] -Building seed filter... [0.009s] -Searching alignments... [0.489s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.381s] -Building query seed array... [0.113s] -Computing hash join... [0.135s] -Building seed filter... [0.01s] -Searching alignments... [0.43s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.321s] -Building query seed array... [0.096s] -Computing hash join... [0.128s] -Building seed filter... [0.009s] -Searching alignments... [0.411s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.311s] -Building query seed array... [0.094s] -Computing hash join... [0.129s] -Building seed filter... [0.008s] -Searching alignments... [0.403s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.361s] -Building query seed array... [0.114s] -Computing hash join... [0.128s] -Building seed filter... [0.009s] -Searching alignments... [0.345s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.378s] -Building query seed array... [0.113s] -Computing hash join... [0.128s] -Building seed filter... [0.008s] -Searching alignments... [0.421s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.317s] -Building query seed array... [0.099s] -Computing hash join... [0.131s] -Building seed filter... [0.009s] -Searching alignments... [0.315s] -Deallocating buffers... [0.094s] -Computing alignments... [8.498s] -Deallocating reference... [0.036s] -Loading reference sequences... [0s] -Deallocating buffers... [0.016s] -Deallocating queries... [0.021s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 21.772s -Reported 440387 pairwise alignments, 443233 HSPs. -22715 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn01_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.925s] -Masking queries... [0.552s] -Building query seed set... [0.049s] -Algorithm: Double-indexed -Building query histograms... [0.186s] -Allocating buffers... [0s] -Loading reference sequences... [1.614s] -Masking reference... [1.056s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.463s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.343s] -Building query seed array... [0.118s] -Computing hash join... [0.143s] -Building seed filter... [0.009s] -Searching alignments... [0.433s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.367s] -Building query seed array... [0.113s] -Computing hash join... [0.129s] -Building seed filter... [0.011s] -Searching alignments... [0.382s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.391s] -Building query seed array... [0.118s] -Computing hash join... [0.134s] -Building seed filter... [0.009s] -Searching alignments... [0.363s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.317s] -Building query seed array... [0.102s] -Computing hash join... [0.131s] -Building seed filter... [0.011s] -Searching alignments... [0.36s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.317s] -Building query seed array... [0.1s] -Computing hash join... [0.128s] -Building seed filter... [0.01s] -Searching alignments... [0.352s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.369s] -Building query seed array... [0.116s] -Computing hash join... [0.126s] -Building seed filter... [0.01s] -Searching alignments... [0.341s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.377s] -Building query seed array... [0.116s] -Computing hash join... [0.134s] -Building seed filter... [0.01s] -Searching alignments... [0.347s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.314s] -Building query seed array... [0.101s] -Computing hash join... [0.13s] -Building seed filter... [0.011s] -Searching alignments... [0.317s] -Deallocating buffers... [0.092s] -Computing alignments... [7.998s] -Deallocating reference... [0.037s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.028s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 21.772s -Reported 405956 pairwise alignments, 409986 HSPs. -21474 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Bv04_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.92s] -Masking queries... [0.256s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.103s] -Allocating buffers... [0s] -Loading reference sequences... [1.588s] -Masking reference... [1.071s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.443s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.345s] -Building query seed array... [0.076s] -Computing hash join... [0.177s] -Building seed filter... [0.008s] -Searching alignments... [0.377s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.07s] -Computing hash join... [0.134s] -Building seed filter... [0.009s] -Searching alignments... [0.331s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.086s] -Computing hash join... [0.135s] -Building seed filter... [0.01s] -Searching alignments... [0.342s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.322s] -Building query seed array... [0.074s] -Computing hash join... [0.132s] -Building seed filter... [0.009s] -Searching alignments... [0.342s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.319s] -Building query seed array... [0.073s] -Computing hash join... [0.135s] -Building seed filter... [0.008s] -Searching alignments... [0.334s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.08s] -Computing hash join... [0.133s] -Building seed filter... [0.008s] -Searching alignments... [0.282s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.385s] -Building query seed array... [0.087s] -Computing hash join... [0.139s] -Building seed filter... [0.008s] -Searching alignments... [0.267s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.317s] -Building query seed array... [0.071s] -Computing hash join... [0.135s] -Building seed filter... [0.009s] -Searching alignments... [0.29s] -Deallocating buffers... [0.093s] -Computing alignments... [7.134s] -Deallocating reference... [0.025s] -Loading reference sequences... [0s] -Deallocating buffers... [0.011s] -Deallocating queries... [0.015s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 18.906s -Reported 537338 pairwise alignments, 538184 HSPs. -28139 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Usac_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [2.187s] -Masking queries... [0.538s] -Building query seed set... [0.04s] -Algorithm: Double-indexed -Building query histograms... [0.206s] -Allocating buffers... [0s] -Loading reference sequences... [1.604s] -Masking reference... [1.049s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.445s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.356s] -Building query seed array... [0.154s] -Computing hash join... [0.154s] -Building seed filter... [0.011s] -Searching alignments... [0.751s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.364s] -Building query seed array... [0.147s] -Computing hash join... [0.136s] -Building seed filter... [0.01s] -Searching alignments... [0.686s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.385s] -Building query seed array... [0.153s] -Computing hash join... [0.144s] -Building seed filter... [0.01s] -Searching alignments... [0.603s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.313s] -Building query seed array... [0.141s] -Computing hash join... [0.15s] -Building seed filter... [0.011s] -Searching alignments... [0.608s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.323s] -Building query seed array... [0.136s] -Computing hash join... [0.144s] -Building seed filter... [0.012s] -Searching alignments... [0.609s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.362s] -Building query seed array... [0.147s] -Computing hash join... [0.141s] -Building seed filter... [0.012s] -Searching alignments... [0.534s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.382s] -Building query seed array... [0.161s] -Computing hash join... [0.142s] -Building seed filter... [0.011s] -Searching alignments... [0.625s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.133s] -Computing hash join... [0.14s] -Building seed filter... [0.01s] -Searching alignments... [0.512s] -Deallocating buffers... [0.091s] -Computing alignments... [12.551s] -Deallocating reference... [0.037s] -Loading reference sequences... [0s] -Deallocating buffers... [0.024s] -Deallocating queries... [0.028s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 28.989s -Reported 725553 pairwise alignments, 730001 HSPs. -36674 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn04_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.543s] -Masking queries... [0.171s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.07s] -Allocating buffers... [0s] -Loading reference sequences... [1.594s] -Masking reference... [1.056s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.483s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.353s] -Building query seed array... [0.07s] -Computing hash join... [0.157s] -Building seed filter... [0.005s] -Searching alignments... [0.158s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.36s] -Building query seed array... [0.05s] -Computing hash join... [0.126s] -Building seed filter... [0.006s] -Searching alignments... [0.147s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.383s] -Building query seed array... [0.059s] -Computing hash join... [0.118s] -Building seed filter... [0.008s] -Searching alignments... [0.15s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.054s] -Computing hash join... [0.115s] -Building seed filter... [0.007s] -Searching alignments... [0.143s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.318s] -Building query seed array... [0.05s] -Computing hash join... [0.108s] -Building seed filter... [0.006s] -Searching alignments... [0.128s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.057s] -Computing hash join... [0.117s] -Building seed filter... [0.007s] -Searching alignments... [0.141s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.378s] -Building query seed array... [0.061s] -Computing hash join... [0.11s] -Building seed filter... [0.006s] -Searching alignments... [0.131s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.326s] -Building query seed array... [0.057s] -Computing hash join... [0.112s] -Building seed filter... [0.006s] -Searching alignments... [0.126s] -Deallocating buffers... [0.095s] -Computing alignments... [3.851s] -Deallocating reference... [0.025s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.008s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 13.385s -Reported 158063 pairwise alignments, 159384 HSPs. -7943 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Emar_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.032s] -Masking queries... [0.268s] -Building query seed set... [0.04s] -Algorithm: Double-indexed -Building query histograms... [0.088s] -Allocating buffers... [0s] -Loading reference sequences... [1.609s] -Masking reference... [1.222s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.44s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.341s] -Building query seed array... [0.074s] -Computing hash join... [0.172s] -Building seed filter... [0.008s] -Searching alignments... [0.338s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.361s] -Building query seed array... [0.068s] -Computing hash join... [0.149s] -Building seed filter... [0.007s] -Searching alignments... [0.291s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.064s] -Computing hash join... [0.136s] -Building seed filter... [0.007s] -Searching alignments... [0.279s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.379s] -Building query seed array... [0.064s] -Computing hash join... [0.136s] -Building seed filter... [0.007s] -Searching alignments... [0.269s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.316s] -Building query seed array... [0.056s] -Computing hash join... [0.133s] -Building seed filter... [0.006s] -Searching alignments... [0.239s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.364s] -Building query seed array... [0.065s] -Computing hash join... [0.128s] -Building seed filter... [0.007s] -Searching alignments... [0.261s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.374s] -Building query seed array... [0.068s] -Computing hash join... [0.134s] -Building seed filter... [0.007s] -Searching alignments... [0.252s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.314s] -Building query seed array... [0.054s] -Computing hash join... [0.131s] -Building seed filter... [0.007s] -Searching alignments... [0.232s] -Deallocating buffers... [0.093s] -Computing alignments... [5.993s] -Deallocating reference... [0.035s] -Loading reference sequences... [0s] -Deallocating buffers... [0.008s] -Deallocating queries... [0.015s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 17.572s -Reported 461440 pairwise alignments, 462438 HSPs. -23164 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Rsp1_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.744s] -Masking queries... [0.211s] -Building query seed set... [0.041s] -Algorithm: Double-indexed -Building query histograms... [0.079s] -Allocating buffers... [0s] -Loading reference sequences... [1.602s] -Masking reference... [1.042s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.478s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.348s] -Building query seed array... [0.057s] -Computing hash join... [0.167s] -Building seed filter... [0.007s] -Searching alignments... [0.237s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.367s] -Building query seed array... [0.062s] -Computing hash join... [0.137s] -Building seed filter... [0.006s] -Searching alignments... [0.222s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.383s] -Building query seed array... [0.064s] -Computing hash join... [0.132s] -Building seed filter... [0.008s] -Searching alignments... [0.214s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.057s] -Computing hash join... [0.132s] -Building seed filter... [0.007s] -Searching alignments... [0.204s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.316s] -Building query seed array... [0.054s] -Computing hash join... [0.127s] -Building seed filter... [0.006s] -Searching alignments... [0.187s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.059s] -Computing hash join... [0.129s] -Building seed filter... [0.006s] -Searching alignments... [0.19s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.374s] -Building query seed array... [0.063s] -Computing hash join... [0.128s] -Building seed filter... [0.008s] -Searching alignments... [0.183s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.322s] -Building query seed array... [0.059s] -Computing hash join... [0.132s] -Building seed filter... [0.008s] -Searching alignments... [0.181s] -Deallocating buffers... [0.092s] -Computing alignments... [4.925s] -Deallocating reference... [0.032s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.011s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 15.334s -Reported 287405 pairwise alignments, 289878 HSPs. -15066 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Sspa_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.639s] -Masking queries... [0.176s] -Building query seed set... [0.042s] -Algorithm: Double-indexed -Building query histograms... [0.083s] -Allocating buffers... [0s] -Loading reference sequences... [1.592s] -Masking reference... [1.04s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.482s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.344s] -Building query seed array... [0.07s] -Computing hash join... [0.161s] -Building seed filter... [0.005s] -Searching alignments... [0.179s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.371s] -Building query seed array... [0.053s] -Computing hash join... [0.117s] -Building seed filter... [0.007s] -Searching alignments... [0.169s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.388s] -Building query seed array... [0.062s] -Computing hash join... [0.11s] -Building seed filter... [0.006s] -Searching alignments... [0.16s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.051s] -Computing hash join... [0.116s] -Building seed filter... [0.006s] -Searching alignments... [0.162s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.321s] -Building query seed array... [0.051s] -Computing hash join... [0.105s] -Building seed filter... [0.006s] -Searching alignments... [0.147s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.056s] -Computing hash join... [0.107s] -Building seed filter... [0.007s] -Searching alignments... [0.146s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.375s] -Building query seed array... [0.059s] -Computing hash join... [0.105s] -Building seed filter... [0.007s] -Searching alignments... [0.153s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.047s] -Computing hash join... [0.106s] -Building seed filter... [0.007s] -Searching alignments... [0.142s] -Deallocating buffers... [0.094s] -Computing alignments... [4.475s] -Deallocating reference... [0.023s] -Loading reference sequences... [0s] -Deallocating buffers... [0.007s] -Deallocating queries... [0.008s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 14.192s -Reported 208347 pairwise alignments, 208875 HSPs. -10555 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Hhir_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.196s] -Masking queries... [0.331s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.12s] -Allocating buffers... [0s] -Loading reference sequences... [1.595s] -Masking reference... [1.25s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.458s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.341s] -Building query seed array... [0.1s] -Computing hash join... [0.146s] -Building seed filter... [0.011s] -Searching alignments... [0.309s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.365s] -Building query seed array... [0.104s] -Computing hash join... [0.137s] -Building seed filter... [0.012s] -Searching alignments... [0.298s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.377s] -Building query seed array... [0.099s] -Computing hash join... [0.128s] -Building seed filter... [0.01s] -Searching alignments... [0.287s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.32s] -Building query seed array... [0.088s] -Computing hash join... [0.134s] -Building seed filter... [0.009s] -Searching alignments... [0.274s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.316s] -Building query seed array... [0.088s] -Computing hash join... [0.126s] -Building seed filter... [0.009s] -Searching alignments... [0.249s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.362s] -Building query seed array... [0.1s] -Computing hash join... [0.129s] -Building seed filter... [0.011s] -Searching alignments... [0.263s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.38s] -Building query seed array... [0.094s] -Computing hash join... [0.128s] -Building seed filter... [0.01s] -Searching alignments... [0.252s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.324s] -Building query seed array... [0.092s] -Computing hash join... [0.129s] -Building seed filter... [0.01s] -Searching alignments... [0.244s] -Deallocating buffers... [0.097s] -Computing alignments... [6.423s] -Deallocating reference... [0.041s] -Loading reference sequences... [0s] -Deallocating buffers... [0.013s] -Deallocating queries... [0.015s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 18.487s -Reported 329599 pairwise alignments, 331231 HSPs. -17423 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn12_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.186s] -Masking queries... [0.323s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.122s] -Allocating buffers... [0s] -Loading reference sequences... [1.602s] -Masking reference... [1.068s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.484s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.344s] -Building query seed array... [0.089s] -Computing hash join... [0.151s] -Building seed filter... [0.01s] -Searching alignments... [0.392s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.087s] -Computing hash join... [0.126s] -Building seed filter... [0.011s] -Searching alignments... [0.275s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.382s] -Building query seed array... [0.09s] -Computing hash join... [0.132s] -Building seed filter... [0.01s] -Searching alignments... [0.271s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.322s] -Building query seed array... [0.087s] -Computing hash join... [0.128s] -Building seed filter... [0.011s] -Searching alignments... [0.261s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.315s] -Building query seed array... [0.081s] -Computing hash join... [0.126s] -Building seed filter... [0.009s] -Searching alignments... [0.235s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.362s] -Building query seed array... [0.092s] -Computing hash join... [0.124s] -Building seed filter... [0.008s] -Searching alignments... [0.253s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.376s] -Building query seed array... [0.092s] -Computing hash join... [0.127s] -Building seed filter... [0.008s] -Searching alignments... [0.243s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.321s] -Building query seed array... [0.107s] -Computing hash join... [0.125s] -Building seed filter... [0.011s] -Searching alignments... [0.225s] -Deallocating buffers... [0.099s] -Computing alignments... [6.156s] -Deallocating reference... [0.036s] -Loading reference sequences... [0s] -Deallocating buffers... [0.014s] -Deallocating queries... [0.018s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 17.975s -Reported 330365 pairwise alignments, 332323 HSPs. -17441 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn14_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [2.193s] -Masking queries... [0.553s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.214s] -Allocating buffers... [0s] -Loading reference sequences... [1.618s] -Masking reference... [1.063s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.459s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.359s] -Building query seed array... [0.158s] -Computing hash join... [0.155s] -Building seed filter... [0.01s] -Searching alignments... [0.505s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.361s] -Building query seed array... [0.15s] -Computing hash join... [0.144s] -Building seed filter... [0.011s] -Searching alignments... [0.476s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.382s] -Building query seed array... [0.151s] -Computing hash join... [0.148s] -Building seed filter... [0.01s] -Searching alignments... [0.448s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.317s] -Building query seed array... [0.13s] -Computing hash join... [0.142s] -Building seed filter... [0.011s] -Searching alignments... [0.445s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.32s] -Building query seed array... [0.133s] -Computing hash join... [0.145s] -Building seed filter... [0.011s] -Searching alignments... [0.394s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.366s] -Building query seed array... [0.15s] -Computing hash join... [0.146s] -Building seed filter... [0.012s] -Searching alignments... [0.422s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.402s] -Building query seed array... [0.16s] -Computing hash join... [0.141s] -Building seed filter... [0.01s] -Searching alignments... [0.4s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.313s] -Building query seed array... [0.136s] -Computing hash join... [0.141s] -Building seed filter... [0.012s] -Searching alignments... [0.386s] -Deallocating buffers... [0.097s] -Computing alignments... [12.415s] -Deallocating reference... [0.038s] -Loading reference sequences... [0s] -Deallocating buffers... [0.021s] -Deallocating queries... [0.029s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 27.503s -Reported 604291 pairwise alignments, 606168 HSPs. -31505 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Gl02_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.803s] -Masking queries... [0.507s] -Building query seed set... [0.05s] -Algorithm: Double-indexed -Building query histograms... [0.156s] -Allocating buffers... [0s] -Loading reference sequences... [1.612s] -Masking reference... [1.068s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.449s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.344s] -Building query seed array... [0.101s] -Computing hash join... [0.247s] -Building seed filter... [0.01s] -Searching alignments... [0.398s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.371s] -Building query seed array... [0.11s] -Computing hash join... [0.124s] -Building seed filter... [0.009s] -Searching alignments... [0.389s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.396s] -Building query seed array... [0.112s] -Computing hash join... [0.133s] -Building seed filter... [0.01s] -Searching alignments... [0.365s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.315s] -Building query seed array... [0.098s] -Computing hash join... [0.13s] -Building seed filter... [0.01s] -Searching alignments... [0.363s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.315s] -Building query seed array... [0.102s] -Computing hash join... [0.132s] -Building seed filter... [0.01s] -Searching alignments... [0.341s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.371s] -Building query seed array... [0.11s] -Computing hash join... [0.13s] -Building seed filter... [0.01s] -Searching alignments... [0.321s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.378s] -Building query seed array... [0.112s] -Computing hash join... [0.13s] -Building seed filter... [0.01s] -Searching alignments... [0.35s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.32s] -Building query seed array... [0.1s] -Computing hash join... [0.127s] -Building seed filter... [0.01s] -Searching alignments... [0.311s] -Deallocating buffers... [0.093s] -Computing alignments... [7.788s] -Deallocating reference... [0.037s] -Loading reference sequences... [0s] -Deallocating buffers... [0.015s] -Deallocating queries... [0.024s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 21.37s -Reported 412048 pairwise alignments, 415577 HSPs. -21731 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Bv05_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.542s] -Masking queries... [0.379s] -Building query seed set... [0.049s] -Algorithm: Double-indexed -Building query histograms... [0.123s] -Allocating buffers... [0s] -Loading reference sequences... [1.582s] -Masking reference... [1.08s] -Initializing temporary storage... [0.013s] -Building reference histograms... [0.476s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.355s] -Building query seed array... [0.099s] -Computing hash join... [0.177s] -Building seed filter... [0.011s] -Searching alignments... [0.378s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.362s] -Building query seed array... [0.087s] -Computing hash join... [0.13s] -Building seed filter... [0.009s] -Searching alignments... [0.354s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.38s] -Building query seed array... [0.093s] -Computing hash join... [0.133s] -Building seed filter... [0.011s] -Searching alignments... [0.338s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.323s] -Building query seed array... [0.089s] -Computing hash join... [0.134s] -Building seed filter... [0.009s] -Searching alignments... [0.344s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.321s] -Building query seed array... [0.084s] -Computing hash join... [0.13s] -Building seed filter... [0.008s] -Searching alignments... [0.317s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.36s] -Building query seed array... [0.112s] -Computing hash join... [0.139s] -Building seed filter... [0.008s] -Searching alignments... [0.297s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.382s] -Building query seed array... [0.09s] -Computing hash join... [0.133s] -Building seed filter... [0.008s] -Searching alignments... [0.324s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.317s] -Building query seed array... [0.085s] -Computing hash join... [0.132s] -Building seed filter... [0.008s] -Searching alignments... [0.281s] -Deallocating buffers... [0.092s] -Computing alignments... [6.871s] -Deallocating reference... [0.038s] -Loading reference sequences... [0s] -Deallocating buffers... [0.011s] -Deallocating queries... [0.02s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 19.663s -Reported 426635 pairwise alignments, 430735 HSPs. -22250 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Bv01_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.369s] -Masking queries... [0.107s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.046s] -Allocating buffers... [0s] -Loading reference sequences... [1.619s] -Masking reference... [1.097s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.461s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.353s] -Building query seed array... [0.043s] -Computing hash join... [0.116s] -Building seed filter... [0.006s] -Searching alignments... [0.109s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.357s] -Building query seed array... [0.034s] -Computing hash join... [0.087s] -Building seed filter... [0.006s] -Searching alignments... [0.119s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.396s] -Building query seed array... [0.04s] -Computing hash join... [0.076s] -Building seed filter... [0.005s] -Searching alignments... [0.104s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.033s] -Computing hash join... [0.077s] -Building seed filter... [0.005s] -Searching alignments... [0.107s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.317s] -Building query seed array... [0.04s] -Computing hash join... [0.078s] -Building seed filter... [0.006s] -Searching alignments... [0.096s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.357s] -Building query seed array... [0.035s] -Computing hash join... [0.077s] -Building seed filter... [0.005s] -Searching alignments... [0.096s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.371s] -Building query seed array... [0.037s] -Computing hash join... [0.077s] -Building seed filter... [0.006s] -Searching alignments... [0.095s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.315s] -Building query seed array... [0.038s] -Computing hash join... [0.075s] -Building seed filter... [0.005s] -Searching alignments... [0.089s] -Deallocating buffers... [0.091s] -Computing alignments... [2.255s] -Deallocating reference... [0.027s] -Loading reference sequences... [0s] -Deallocating buffers... [0.003s] -Deallocating queries... [0.007s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 10.778s -Reported 119039 pairwise alignments, 121169 HSPs. -5832 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Slin_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.775s] -Masking queries... [0.471s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.174s] -Allocating buffers... [0s] -Loading reference sequences... [1.598s] -Masking reference... [1.039s] -Initializing temporary storage... [0.012s] -Building reference histograms... [0.468s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.351s] -Building query seed array... [0.136s] -Computing hash join... [0.16s] -Building seed filter... [0.012s] -Searching alignments... [0.495s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.372s] -Building query seed array... [0.129s] -Computing hash join... [0.145s] -Building seed filter... [0.01s] -Searching alignments... [0.481s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.378s] -Building query seed array... [0.129s] -Computing hash join... [0.144s] -Building seed filter... [0.012s] -Searching alignments... [0.451s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.315s] -Building query seed array... [0.119s] -Computing hash join... [0.144s] -Building seed filter... [0.013s] -Searching alignments... [0.441s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.321s] -Building query seed array... [0.114s] -Computing hash join... [0.145s] -Building seed filter... [0.012s] -Searching alignments... [0.386s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.362s] -Building query seed array... [0.136s] -Computing hash join... [0.151s] -Building seed filter... [0.013s] -Searching alignments... [0.388s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.139s] -Computing hash join... [0.144s] -Building seed filter... [0.014s] -Searching alignments... [0.389s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.314s] -Building query seed array... [0.126s] -Computing hash join... [0.149s] -Building seed filter... [0.012s] -Searching alignments... [0.364s] -Deallocating buffers... [0.095s] -Computing alignments... [11.681s] -Deallocating reference... [0.036s] -Loading reference sequences... [0s] -Deallocating buffers... [0.021s] -Deallocating queries... [0.028s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 25.969s -Reported 640067 pairwise alignments, 641506 HSPs. -32752 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Gl03_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.801s] -Masking queries... [0.495s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.18s] -Allocating buffers... [0s] -Loading reference sequences... [1.586s] -Masking reference... [1.057s] -Initializing temporary storage... [0.013s] -Building reference histograms... [0.47s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.345s] -Building query seed array... [0.135s] -Computing hash join... [0.166s] -Building seed filter... [0.01s] -Searching alignments... [0.68s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.371s] -Building query seed array... [0.136s] -Computing hash join... [0.14s] -Building seed filter... [0.012s] -Searching alignments... [0.5s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.383s] -Building query seed array... [0.142s] -Computing hash join... [0.139s] -Building seed filter... [0.01s] -Searching alignments... [0.596s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.317s] -Building query seed array... [0.127s] -Computing hash join... [0.144s] -Building seed filter... [0.01s] -Searching alignments... [0.585s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.315s] -Building query seed array... [0.118s] -Computing hash join... [0.139s] -Building seed filter... [0.01s] -Searching alignments... [0.566s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.363s] -Building query seed array... [0.133s] -Computing hash join... [0.139s] -Building seed filter... [0.01s] -Searching alignments... [0.462s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.379s] -Building query seed array... [0.133s] -Computing hash join... [0.143s] -Building seed filter... [0.011s] -Searching alignments... [0.587s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.316s] -Building query seed array... [0.116s] -Computing hash join... [0.138s] -Building seed filter... [0.011s] -Searching alignments... [0.379s] -Deallocating buffers... [0.095s] -Computing alignments... [10.458s] -Deallocating reference... [0.034s] -Loading reference sequences... [0s] -Deallocating buffers... [0.021s] -Deallocating queries... [0.018s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 25.722s -Reported 592579 pairwise alignments, 596988 HSPs. -30042 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn09_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [1.276s] -Masking queries... [0.366s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.132s] -Allocating buffers... [0s] -Loading reference sequences... [1.59s] -Masking reference... [1.132s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.465s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.352s] -Building query seed array... [0.11s] -Computing hash join... [0.147s] -Building seed filter... [0.008s] -Searching alignments... [0.452s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.362s] -Building query seed array... [0.108s] -Computing hash join... [0.131s] -Building seed filter... [0.008s] -Searching alignments... [0.364s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.375s] -Building query seed array... [0.102s] -Computing hash join... [0.13s] -Building seed filter... [0.008s] -Searching alignments... [0.328s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.319s] -Building query seed array... [0.103s] -Computing hash join... [0.132s] -Building seed filter... [0.008s] -Searching alignments... [0.4s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.327s] -Building query seed array... [0.092s] -Computing hash join... [0.129s] -Building seed filter... [0.009s] -Searching alignments... [0.283s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.368s] -Building query seed array... [0.102s] -Computing hash join... [0.125s] -Building seed filter... [0.009s] -Searching alignments... [0.303s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.377s] -Building query seed array... [0.112s] -Computing hash join... [0.129s] -Building seed filter... [0.009s] -Searching alignments... [0.33s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.318s] -Building query seed array... [0.092s] -Computing hash join... [0.127s] -Building seed filter... [0.009s] -Searching alignments... [0.276s] -Deallocating buffers... [0.093s] -Computing alignments... [7.313s] -Deallocating reference... [0.039s] -Loading reference sequences... [0s] -Deallocating buffers... [0.016s] -Deallocating queries... [0.019s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 19.997s -Reported 381006 pairwise alignments, 382593 HSPs. -19632 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Nn13_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps/DiamondOG -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = ../Databases/db_OG/Hook-6.5.dmnd -Sequences = 1512043 -Letters = 714797884 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.152s] -Masking queries... [0.062s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.032s] -Allocating buffers... [0s] -Loading reference sequences... [1.616s] -Masking reference... [1.285s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.457s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.351s] -Building query seed array... [0.028s] -Computing hash join... [0.069s] -Building seed filter... [0.004s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.357s] -Building query seed array... [0.024s] -Computing hash join... [0.058s] -Building seed filter... [0.004s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.37s] -Building query seed array... [0.022s] -Computing hash join... [0.054s] -Building seed filter... [0.004s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.32s] -Building query seed array... [0.029s] -Computing hash join... [0.056s] -Building seed filter... [0.004s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.313s] -Building query seed array... [0.027s] -Computing hash join... [0.054s] -Building seed filter... [0.004s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.358s] -Building query seed array... [0.026s] -Computing hash join... [0.056s] -Building seed filter... [0.004s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.374s] -Building query seed array... [0.023s] -Computing hash join... [0.05s] -Building seed filter... [0.004s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.314s] -Building query seed array... [0.025s] -Computing hash join... [0.052s] -Building seed filter... [0.004s] -Searching alignments... [0.029s] -Deallocating buffers... [0.092s] -Computing alignments... [0.366s] -Deallocating reference... [0.03s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0.001s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 7.863s -Reported 22784 pairwise alignments, 23612 HSPs. -1572 queries aligned. - -Starting to "BLAST" against OG databases - - -"BLAST"-ing against OG database using DIAMOND: Hook-6.5.dmnd - - - - -Processing OG-database results to keep only the BEST match for each transcript - - -Updating Fasta File Sequence Names with their BEST OG hits - - - -Look for Sr_rh_Atps_WTA_EPUWTA_EPU.fasta in the ../beegfs/ Folder - - -Next Script is: 4_InFrameStopFreq.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.036s] -Masking queries... [0.024s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.106s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.054s] -Building query seed array... [0.009s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.057s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.038s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.049s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.009s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.012s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.049s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.046s] -Building query seed array... [0.01s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.052s] -Deallocating buffers... [0.01s] -Computing alignments... [0.462s] -Deallocating reference... [0.002s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.89s -Reported 14977 pairwise alignments, 14985 HSPs. -14977 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.026s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.103s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.071s] -Building query seed array... [0.019s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.06s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.068s] -Building query seed array... [0.024s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.024s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.05s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.058s] -Building query seed array... [0.021s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.053s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.06s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.021s] -Computing hash join... [0.008s] -Building seed filter... [0.005s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.056s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.052s] -Deallocating buffers... [0.011s] -Computing alignments... [0.475s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.101s -Reported 14970 pairwise alignments, 14978 HSPs. -14970 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.023s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.013s] -Allocating buffers... [0s] -Loading reference sequences... [0.147s] -Masking reference... [0.107s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.066s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.066s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.048s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.015s] -Computing hash join... [0.009s] -Building seed filter... [0.004s] -Searching alignments... [0.05s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.068s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.061s] -Building query seed array... [0.019s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.056s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.009s] -Computing alignments... [0.471s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.991s -Reported 14951 pairwise alignments, 14957 HSPs. -14951 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn02_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.015s] -Masking queries... [0.022s] -Building query seed set... [0.026s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.153s] -Masking reference... [0.105s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.013s] -Computing hash join... [0.015s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.01s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.007s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.016s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.007s] -Deallocating buffers... [0.008s] -Computing alignments... [0.183s] -Deallocating reference... [0.005s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.369s -Reported 5809 pairwise alignments, 5814 HSPs. -5809 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.015s] -Masking queries... [0.017s] -Building query seed set... [0.019s] -Algorithm: Double-indexed -Building query histograms... [0.008s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.103s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.065s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.066s] -Building query seed array... [0.015s] -Computing hash join... [0.017s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.013s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.063s] -Building query seed array... [0.016s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.059s] -Building query seed array... [0.012s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.01s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.01s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.013s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.011s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Deallocating buffers... [0.008s] -Computing alignments... [0.183s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.378s -Reported 5801 pairwise alignments, 5806 HSPs. -5801 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.015s] -Masking queries... [0.02s] -Building query seed set... [0.02s] -Algorithm: Double-indexed -Building query histograms... [0.011s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.108s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.018s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.012s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.012s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.01s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Deallocating buffers... [0.01s] -Computing alignments... [0.184s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.354s -Reported 5802 pairwise alignments, 5807 HSPs. -5802 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Gspa_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.026s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.108s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.044s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.067s] -Building query seed array... [0.021s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.06s] -Building query seed array... [0.024s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.02s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.02s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.061s] -Building query seed array... [0.025s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.008s] -Computing alignments... [0.452s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.912s -Reported 16011 pairwise alignments, 16017 HSPs. -16011 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.033s] -Masking queries... [0.067s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.017s] -Allocating buffers... [0s] -Loading reference sequences... [0.146s] -Masking reference... [0.104s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.061s] -Building query seed array... [0.009s] -Computing hash join... [0.018s] -Building seed filter... [0.004s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.038s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.04s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.041s] -Building query seed array... [0.011s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.046s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.008s] -Computing alignments... [0.452s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.802s -Reported 15989 pairwise alignments, 15994 HSPs. -15989 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.023s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.104s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.069s] -Building query seed array... [0.018s] -Computing hash join... [0.018s] -Building seed filter... [0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.041s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.049s] -Building query seed array... [0.019s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.051s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.005s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.016s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.007s] -Computing alignments... [0.451s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.823s -Reported 16009 pairwise alignments, 16014 HSPs. -16009 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn06_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.034s] -Masking queries... [0.031s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.021s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.121s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.057s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.069s] -Building query seed array... [0.028s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.061s] -Building query seed array... [0.021s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.022s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.066s] -Building query seed array... [0.023s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.021s] -Deallocating buffers... [0.007s] -Computing alignments... [0.473s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.944s -Reported 19508 pairwise alignments, 19511 HSPs. -19508 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.036s] -Masking queries... [0.025s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.147s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.02s] -Computing hash join... [0.018s] -Building seed filter... [0.003s] -Searching alignments... [0.055s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.063s] -Building query seed array... [0.024s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.044s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.077s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.053s] -Building query seed array... [0.021s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.056s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.024s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.064s] -Building query seed array... [0.022s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.025s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Deallocating buffers... [0.007s] -Computing alignments... [0.481s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.992s -Reported 19456 pairwise alignments, 19460 HSPs. -19456 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.035s] -Masking queries... [0.026s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.106s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.057s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.048s] -Building query seed array... [0.011s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.041s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.045s] -Building query seed array... [0.012s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.045s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.042s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.007s] -Computing alignments... [0.471s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.796s -Reported 19448 pairwise alignments, 19452 HSPs. -19448 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Bv02_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.022s] -Masking queries... [0.024s] -Building query seed set... [0.025s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.145s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.052s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.061s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.062s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.062s] -Building query seed array... [0.021s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.061s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.059s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.061s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.045s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.012s] -Deallocating buffers... [0.008s] -Computing alignments... [0.29s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.596s -Reported 9114 pairwise alignments, 9130 HSPs. -9114 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.025s] -Masking queries... [0.025s] -Building query seed set... [0.025s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.06s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.054s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.068s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.02s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Deallocating buffers... [0.008s] -Computing alignments... [0.288s] -Deallocating reference... [0.002s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.586s -Reported 9086 pairwise alignments, 9105 HSPs. -9086 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.025s] -Masking queries... [0.024s] -Building query seed set... [0.026s] -Algorithm: Double-indexed -Building query histograms... [0.013s] -Allocating buffers... [0s] -Loading reference sequences... [0.146s] -Masking reference... [0.111s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.057s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.046s] -Building query seed array... [0.018s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.015s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Deallocating buffers... [0.009s] -Computing alignments... [0.282s] -Deallocating reference... [0.002s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.536s -Reported 9098 pairwise alignments, 9119 HSPs. -9098 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Hind_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.026s] -Masking queries... [0.022s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.011s] -Allocating buffers... [0s] -Loading reference sequences... [0.145s] -Masking reference... [0.107s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.059s] -Building query seed array... [0.016s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.038s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.065s] -Building query seed array... [0.016s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.063s] -Building query seed array... [0.02s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.016s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.052s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.005s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.042s] -Building query seed array... [0.013s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.008s] -Computing alignments... [0.339s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.721s -Reported 13395 pairwise alignments, 13400 HSPs. -13395 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.024s] -Building query seed set... [0.031s] -Algorithm: Double-indexed -Building query histograms... [0.016s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.106s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.06s] -Building query seed array... [0.009s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.047s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.012s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.041s] -Building query seed array... [0.011s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.037s] -Building query seed array... [0.009s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.049s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.049s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.004s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.038s] -Building query seed array... [0.009s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.008s] -Computing alignments... [0.35s] -Deallocating reference... [0.002s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.588s -Reported 13387 pairwise alignments, 13390 HSPs. -13387 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.026s] -Masking queries... [0.025s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.147s] -Masking reference... [0.105s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.061s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.016s] -Computing hash join... [0.014s] -Building seed filter... [0.005s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.021s] -Computing hash join... [0.013s] -Building seed filter... [0.004s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.059s] -Building query seed array... [0.019s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.017s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.016s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Deallocating buffers... [0.007s] -Computing alignments... [0.356s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.724s -Reported 13378 pairwise alignments, 13382 HSPs. -13378 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn11_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.034s] -Masking queries... [0.025s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.017s] -Allocating buffers... [0s] -Loading reference sequences... [0.147s] -Masking reference... [0.105s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.058s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.06s] -Building query seed array... [0.014s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.044s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.059s] -Building query seed array... [0.024s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.019s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.048s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.02s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.02s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.007s] -Computing alignments... [0.448s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.832s -Reported 18677 pairwise alignments, 18682 HSPs. -18677 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.034s] -Masking queries... [0.025s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.145s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.058s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.022s] -Computing hash join... [0.015s] -Building seed filter... [0.003s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.026s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.038s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.021s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.055s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.022s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Deallocating buffers... [0.007s] -Computing alignments... [0.463s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.88s -Reported 18645 pairwise alignments, 18651 HSPs. -18645 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.034s] -Masking queries... [0.026s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.146s] -Masking reference... [0.104s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.059s] -Building query seed array... [0.021s] -Computing hash join... [0.017s] -Building seed filter... [0.003s] -Searching alignments... [0.051s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.066s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.021s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.043s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.023s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.064s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.022s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Deallocating buffers... [0.007s] -Computing alignments... [0.457s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.926s -Reported 18616 pairwise alignments, 18622 HSPs. -18616 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Bv03_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.017s] -Masking queries... [0.019s] -Building query seed set... [0.02s] -Algorithm: Double-indexed -Building query histograms... [0.008s] -Allocating buffers... [0s] -Loading reference sequences... [0.146s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.059s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.005s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.046s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.048s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.065s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Deallocating buffers... [0.008s] -Computing alignments... [0.248s] -Deallocating reference... [0.005s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.483s -Reported 7264 pairwise alignments, 7269 HSPs. -7264 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.018s] -Masking queries... [0.022s] -Building query seed set... [0.024s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.145s] -Masking reference... [0.104s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.065s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.013s] -Computing hash join... [0.015s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.018s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.01s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Deallocating buffers... [0.009s] -Computing alignments... [0.25s] -Deallocating reference... [0.005s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.505s -Reported 7257 pairwise alignments, 7263 HSPs. -7257 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.019s] -Masking queries... [0.017s] -Building query seed set... [0.02s] -Algorithm: Double-indexed -Building query histograms... [0.011s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.105s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.052s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.061s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.06s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.012s] -Computing hash join... [0.013s] -Building seed filter... [0.004s] -Searching alignments... [0.008s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.045s] -Building query seed array... [0.011s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Deallocating buffers... [0.008s] -Computing alignments... [0.244s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.462s -Reported 7266 pairwise alignments, 7272 HSPs. -7266 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Gsp1_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.019s] -Masking queries... [0.021s] -Building query seed set... [0.019s] -Algorithm: Double-indexed -Building query histograms... [0.008s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.063s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.064s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.043s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.013s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Deallocating buffers... [0.007s] -Computing alignments... [0.256s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.523s -Reported 10678 pairwise alignments, 10680 HSPs. -10678 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.024s] -Masking queries... [0.024s] -Building query seed set... [0.023s] -Algorithm: Double-indexed -Building query histograms... [0.009s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.105s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.059s] -Building query seed array... [0.012s] -Computing hash join... [0.014s] -Building seed filter... [0.006s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.061s] -Building query seed array... [0.016s] -Computing hash join... [0.015s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.061s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.045s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Deallocating buffers... [0.007s] -Computing alignments... [0.257s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.54s -Reported 10650 pairwise alignments, 10652 HSPs. -10650 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.02s] -Masking queries... [0.02s] -Building query seed set... [0.028s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.053s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.057s] -Building query seed array... [0.011s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.059s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.013s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.054s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.063s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Deallocating buffers... [0.007s] -Computing alignments... [0.265s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.55s -Reported 10635 pairwise alignments, 10637 HSPs. -10635 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Bv06_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.001s] -Masking queries... [0.015s] -Building query seed set... [0.003s] -Algorithm: Double-indexed -Building query histograms... [0.002s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.119s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.063s] -Building query seed array... [0.009s] -Computing hash join... [0.012s] -Building seed filter... [0.005s] -Searching alignments... [0.006s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.012s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.006s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.011s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.009s] -Computing hash join... [0.01s] -Building seed filter... [0.007s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.044s] -Building query seed array... [0.008s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.005s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.008s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.003s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.009s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.008s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.003s] -Deallocating buffers... [0.007s] -Computing alignments... [0.054s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.1s -Reported 1110 pairwise alignments, 1110 HSPs. -1110 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.001s] -Masking queries... [0.014s] -Building query seed set... [0.002s] -Algorithm: Double-indexed -Building query histograms... [0.002s] -Allocating buffers... [0s] -Loading reference sequences... [0.155s] -Masking reference... [0.133s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.058s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.067s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.006s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.013s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.01s] -Computing hash join... [0.01s] -Building seed filter... [0.005s] -Searching alignments... [0.005s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.009s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.005s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.009s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.003s] -Deallocating buffers... [0.007s] -Computing alignments... [0.053s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.135s -Reported 1110 pairwise alignments, 1110 HSPs. -1110 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.003s] -Masking queries... [0.013s] -Building query seed set... [0.003s] -Algorithm: Double-indexed -Building query histograms... [0.002s] -Allocating buffers... [0s] -Loading reference sequences... [0.147s] -Masking reference... [0.109s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.059s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.061s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.006s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.062s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.008s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.007s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.055s] -Building query seed array... [0.009s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.003s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.011s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.009s] -Computing hash join... [0.013s] -Building seed filter... [0.004s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.062s] -Building query seed array... [0.01s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.003s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.053s] -Building query seed array... [0.009s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.003s] -Deallocating buffers... [0.008s] -Computing alignments... [0.056s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.139s -Reported 1110 pairwise alignments, 1110 HSPs. -1110 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Gl01_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.019s] -Masking queries... [0.018s] -Building query seed set... [0.02s] -Algorithm: Double-indexed -Building query histograms... [0.008s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.112s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.066s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.013s] -Computing hash join... [0.015s] -Building seed filter... [0.006s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.053s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.051s] -Building query seed array... [0.013s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.062s] -Building query seed array... [0.019s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.055s] -Building query seed array... [0.011s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Deallocating buffers... [0.007s] -Computing alignments... [0.232s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.506s -Reported 8949 pairwise alignments, 8950 HSPs. -8949 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.019s] -Masking queries... [0.022s] -Building query seed set... [0.02s] -Algorithm: Double-indexed -Building query histograms... [0.008s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.068s] -Building query seed array... [0.013s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.046s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Deallocating buffers... [0.009s] -Computing alignments... [0.242s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.483s -Reported 8938 pairwise alignments, 8939 HSPs. -8938 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.019s] -Masking queries... [0.017s] -Building query seed set... [0.02s] -Algorithm: Double-indexed -Building query histograms... [0.009s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.104s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.058s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.066s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.064s] -Building query seed array... [0.021s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.061s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.044s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.005s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Deallocating buffers... [0.007s] -Computing alignments... [0.238s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.497s -Reported 8940 pairwise alignments, 8941 HSPs. -8940 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Esca_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.021s] -Masking queries... [0.025s] -Building query seed set... [0.024s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.147s] -Masking reference... [0.106s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.063s] -Building query seed array... [0.016s] -Computing hash join... [0.014s] -Building seed filter... [0.004s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.017s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Deallocating buffers... [0.007s] -Computing alignments... [0.277s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.541s -Reported 8489 pairwise alignments, 8494 HSPs. -8489 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.03s] -Masking queries... [0.024s] -Building query seed set... [0.025s] -Algorithm: Double-indexed -Building query histograms... [0.018s] -Allocating buffers... [0s] -Loading reference sequences... [0.152s] -Masking reference... [0.112s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.014s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.058s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.049s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.013s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.057s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.061s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Deallocating buffers... [0.012s] -Computing alignments... [0.28s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.575s -Reported 8457 pairwise alignments, 8463 HSPs. -8457 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.026s] -Masking queries... [0.021s] -Building query seed set... [0.025s] -Algorithm: Double-indexed -Building query histograms... [0.009s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.111s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.013s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.015s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.046s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.047s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.01s] -Deallocating buffers... [0.008s] -Computing alignments... [0.271s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.522s -Reported 8493 pairwise alignments, 8499 HSPs. -8493 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Calb_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.019s] -Masking queries... [0.021s] -Building query seed set... [0.022s] -Algorithm: Double-indexed -Building query histograms... [0.016s] -Allocating buffers... [0s] -Loading reference sequences... [0.155s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.065s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.005s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.005s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.049s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.019s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.01s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Deallocating buffers... [0.008s] -Computing alignments... [0.243s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.499s -Reported 7656 pairwise alignments, 7658 HSPs. -7656 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.025s] -Masking queries... [0.021s] -Building query seed set... [0.022s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.104s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.051s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.01s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Deallocating buffers... [0.009s] -Computing alignments... [0.245s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.459s -Reported 7627 pairwise alignments, 7629 HSPs. -7627 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.024s] -Masking queries... [0.02s] -Building query seed set... [0.021s] -Algorithm: Double-indexed -Building query histograms... [0.012s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.112s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.06s] -Building query seed array... [0.012s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.058s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.019s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.062s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.054s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Deallocating buffers... [0.008s] -Computing alignments... [0.243s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.525s -Reported 7662 pairwise alignments, 7664 HSPs. -7662 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Emac_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.026s] -Masking queries... [0.032s] -Building query seed set... [0.031s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.058s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.063s] -Building query seed array... [0.015s] -Computing hash join... [0.019s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.061s] -Building query seed array... [0.019s] -Computing hash join... [0.015s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.061s] -Building query seed array... [0.02s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.013s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.06s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.016s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.007s] -Computing alignments... [0.373s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.759s -Reported 13827 pairwise alignments, 13830 HSPs. -13827 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.027s] -Masking queries... [0.024s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.102s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.067s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.063s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.06s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.023s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.044s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.053s] -Building query seed array... [0.02s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.021s] -Deallocating buffers... [0.007s] -Computing alignments... [0.383s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.757s -Reported 13833 pairwise alignments, 13835 HSPs. -13833 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.027s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.114s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.016s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.074s] -Building query seed array... [0.023s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.038s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.061s] -Building query seed array... [0.021s] -Computing hash join... [0.014s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.059s] -Building query seed array... [0.019s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.049s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.06s] -Building query seed array... [0.024s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.058s] -Building query seed array... [0.019s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.008s] -Computing alignments... [0.378s] -Deallocating reference... [0.005s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.822s -Reported 13823 pairwise alignments, 13825 HSPs. -13823 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn05_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.033s] -Masking queries... [0.028s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.019s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.106s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.017s] -Computing hash join... [0.015s] -Building seed filter... [0.003s] -Searching alignments... [0.057s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.023s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.061s] -Building query seed array... [0.023s] -Computing hash join... [0.009s] -Building seed filter... [0.004s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.044s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.054s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.016s] -Computing hash join... [0.009s] -Building seed filter... [0.004s] -Searching alignments... [0.022s] -Deallocating buffers... [0.008s] -Computing alignments... [0.54s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.997s -Reported 16657 pairwise alignments, 16661 HSPs. -16657 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.034s] -Masking queries... [0.037s] -Building query seed set... [0.044s] -Algorithm: Double-indexed -Building query histograms... [0.016s] -Allocating buffers... [0s] -Loading reference sequences... [0.152s] -Masking reference... [0.106s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.02s] -Computing hash join... [0.012s] -Building seed filter... [0.007s] -Searching alignments... [0.058s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.059s] -Building query seed array... [0.02s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.043s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.02s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.014s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.046s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.017s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Deallocating buffers... [0.007s] -Computing alignments... [0.536s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.985s -Reported 16447 pairwise alignments, 16451 HSPs. -16447 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.033s] -Masking queries... [0.025s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.017s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.104s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.019s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.056s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.061s] -Building query seed array... [0.025s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.043s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.06s] -Building query seed array... [0.027s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.062s] -Building query seed array... [0.021s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.021s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.023s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.063s] -Building query seed array... [0.023s] -Computing hash join... [0.008s] -Building seed filter... [0.004s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Deallocating buffers... [0.009s] -Computing alignments... [0.534s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.049s -Reported 16439 pairwise alignments, 16443 HSPs. -16439 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn10_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.026s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.019s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.049s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.017s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.045s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.017s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.007s] -Computing alignments... [0.409s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.746s -Reported 14708 pairwise alignments, 14710 HSPs. -14708 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.036s] -Masking queries... [0.025s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.012s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.107s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.016s] -Computing hash join... [0.015s] -Building seed filter... [0.003s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.058s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.02s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.06s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.02s] -Deallocating buffers... [0.008s] -Computing alignments... [0.422s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.804s -Reported 14686 pairwise alignments, 14687 HSPs. -14686 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.03s] -Masking queries... [0.032s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.013s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.107s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.016s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.046s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.067s] -Building query seed array... [0.022s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.038s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.062s] -Building query seed array... [0.024s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.021s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.059s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.018s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.019s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Deallocating buffers... [0.007s] -Computing alignments... [0.419s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.822s -Reported 14707 pairwise alignments, 14709 HSPs. -14707 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn03_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.103s] -Building query seed set... [0.027s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.147s] -Masking reference... [0.112s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.059s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.018s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.02s] -Computing hash join... [0.007s] -Building seed filter... [0.004s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.042s] -Building query seed array... [0.013s] -Computing hash join... [0.006s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.018s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.023s] -Computing hash join... [0.006s] -Building seed filter... [0.004s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.02s] -Computing hash join... [0.007s] -Building seed filter... [0.004s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.019s] -Computing hash join... [0.007s] -Building seed filter... [0.004s] -Searching alignments... [0.014s] -Deallocating buffers... [0.007s] -Computing alignments... [0.406s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.813s -Reported 12458 pairwise alignments, 12469 HSPs. -12458 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.027s] -Building query seed set... [0.027s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.146s] -Masking reference... [0.107s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.067s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.017s] -Computing hash join... [0.008s] -Building seed filter... [0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.017s] -Computing hash join... [0.008s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.016s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.017s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.059s] -Building query seed array... [0.019s] -Computing hash join... [0.008s] -Building seed filter... [0.004s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.022s] -Computing hash join... [0.006s] -Building seed filter... [0.004s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.045s] -Building query seed array... [0.018s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Deallocating buffers... [0.007s] -Computing alignments... [0.412s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.745s -Reported 12438 pairwise alignments, 12449 HSPs. -12438 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.026s] -Building query seed set... [0.028s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.146s] -Masking reference... [0.108s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.061s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.02s] -Computing hash join... [0.008s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.018s] -Computing hash join... [0.009s] -Building seed filter... [0.004s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.062s] -Building query seed array... [0.02s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.057s] -Building query seed array... [0.02s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.016s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.018s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.063s] -Building query seed array... [0.018s] -Computing hash join... [0.006s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.018s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Deallocating buffers... [0.008s] -Computing alignments... [0.4s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.78s -Reported 12459 pairwise alignments, 12473 HSPs. -12459 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Halb_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.023s] -Building query seed set... [0.022s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.106s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.059s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.065s] -Building query seed array... [0.014s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.067s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.016s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.043s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.125s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.064s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.013s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Deallocating buffers... [0.008s] -Computing alignments... [0.376s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.834s -Reported 13085 pairwise alignments, 13089 HSPs. -13085 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.026s] -Masking queries... [0.022s] -Building query seed set... [0.021s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.105s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.045s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.013s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.062s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.06s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.057s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.052s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.133s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.068s] -Building query seed array... [0.016s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.067s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.053s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Deallocating buffers... [0.008s] -Computing alignments... [0.378s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.875s -Reported 13082 pairwise alignments, 13085 HSPs. -13082 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.022s] -Masking queries... [0.024s] -Building query seed set... [0.023s] -Algorithm: Double-indexed -Building query histograms... [0.012s] -Allocating buffers... [0s] -Loading reference sequences... [0.152s] -Masking reference... [0.107s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.065s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.046s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.059s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.016s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.011s] -Computing hash join... [0.008s] -Building seed filter... [0.003s] -Searching alignments... [0.119s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.063s] -Building query seed array... [0.016s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.042s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Deallocating buffers... [0.007s] -Computing alignments... [0.379s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.802s -Reported 13075 pairwise alignments, 13079 HSPs. -13075 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn08_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.034s] -Masking queries... [0.032s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.058s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.059s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.056s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.013s] -Computing hash join... [0.008s] -Building seed filter... [0.003s] -Searching alignments... [0.062s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.06s] -Building query seed array... [0.013s] -Computing hash join... [0.006s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.011s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.06s] -Building query seed array... [0.012s] -Computing hash join... [0.006s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.012s] -Computing hash join... [0.006s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.018s] -Computing hash join... [0.007s] -Building seed filter... [0.004s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.011s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Deallocating buffers... [0.009s] -Computing alignments... [0.496s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.894s -Reported 16992 pairwise alignments, 17022 HSPs. -16992 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.035s] -Masking queries... [0.025s] -Building query seed set... [0.027s] -Algorithm: Double-indexed -Building query histograms... [0.018s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.107s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.011s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.057s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.013s] -Computing hash join... [0.009s] -Building seed filter... [0.004s] -Searching alignments... [0.054s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.013s] -Computing hash join... [0.008s] -Building seed filter... [0.004s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.01s] -Computing hash join... [0.008s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.012s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.045s] -Building query seed array... [0.012s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.048s] -Building query seed array... [0.012s] -Computing hash join... [0.007s] -Building seed filter... [0.004s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.011s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Deallocating buffers... [0.008s] -Computing alignments... [0.498s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.821s -Reported 16995 pairwise alignments, 17026 HSPs. -16995 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.035s] -Masking queries... [0.027s] -Building query seed set... [0.028s] -Algorithm: Double-indexed -Building query histograms... [0.019s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.105s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.061s] -Building query seed array... [0.011s] -Computing hash join... [0.009s] -Building seed filter... [0.004s] -Searching alignments... [0.053s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.015s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.059s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.011s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.012s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.044s] -Building query seed array... [0.013s] -Computing hash join... [0.007s] -Building seed filter... [0.004s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.048s] -Building query seed array... [0.012s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.049s] -Building query seed array... [0.011s] -Computing hash join... [0.007s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.012s] -Computing hash join... [0.007s] -Building seed filter... [0.004s] -Searching alignments... [0.024s] -Deallocating buffers... [0.008s] -Computing alignments... [0.497s] -Deallocating reference... [0.002s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.825s -Reported 17008 pairwise alignments, 17039 HSPs. -17008 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Tx01_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.05s] -Masking queries... [0.034s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.018s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.122s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.061s] -Building query seed array... [0.013s] -Computing hash join... [0.015s] -Building seed filter... [0.003s] -Searching alignments... [0.063s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.044s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.04s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.042s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.041s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.047s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.039s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Deallocating buffers... [0.007s] -Computing alignments... [0.514s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.903s -Reported 19505 pairwise alignments, 19510 HSPs. -19505 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.043s] -Masking queries... [0.038s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.018s] -Allocating buffers... [0s] -Loading reference sequences... [0.144s] -Masking reference... [0.114s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.058s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.063s] -Building query seed array... [0.021s] -Computing hash join... [0.016s] -Building seed filter... [0.004s] -Searching alignments... [0.064s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.062s] -Building query seed array... [0.022s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.074s] -Building query seed array... [0.026s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.066s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.043s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.023s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.061s] -Building query seed array... [0.02s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Deallocating buffers... [0.007s] -Computing alignments... [0.532s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.098s -Reported 19471 pairwise alignments, 19474 HSPs. -19471 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.04s] -Masking queries... [0.026s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.016s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.105s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.052s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.06s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.061s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.061s] -Building query seed array... [0.021s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.049s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.049s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.021s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.045s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Deallocating buffers... [0.007s] -Computing alignments... [0.52s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.964s -Reported 19449 pairwise alignments, 19453 HSPs. -19449 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn07_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.035s] -Masking queries... [0.026s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.017s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.104s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.01s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.055s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.044s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.062s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.014s] -Computing hash join... [0.009s] -Building seed filter... [0.004s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.045s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.04s] -Building query seed array... [0.009s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.025s] -Deallocating buffers... [0.009s] -Computing alignments... [0.515s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.892s -Reported 18653 pairwise alignments, 18661 HSPs. -18653 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.044s] -Masking queries... [0.03s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.016s] -Allocating buffers... [0s] -Loading reference sequences... [0.152s] -Masking reference... [0.115s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.053s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.06s] -Building query seed array... [0.011s] -Computing hash join... [0.009s] -Building seed filter... [0.004s] -Searching alignments... [0.055s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.016s] -Computing hash join... [0.013s] -Building seed filter... [0.005s] -Searching alignments... [0.048s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.049s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Deallocating buffers... [0.009s] -Computing alignments... [0.527s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.96s -Reported 18645 pairwise alignments, 18655 HSPs. -18645 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.036s] -Masking queries... [0.028s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.017s] -Allocating buffers... [0s] -Loading reference sequences... [0.152s] -Masking reference... [0.106s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.006s] -Searching alignments... [0.057s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.039s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.043s] -Building query seed array... [0.01s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.046s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.005s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.012s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.038s] -Building query seed array... [0.011s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Deallocating buffers... [0.008s] -Computing alignments... [0.525s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.873s -Reported 18646 pairwise alignments, 18653 HSPs. -18646 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn01_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.033s] -Masking queries... [0.025s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.017s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.105s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.052s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.059s] -Building query seed array... [0.022s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.063s] -Building query seed array... [0.027s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.058s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.021s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Deallocating buffers... [0.007s] -Computing alignments... [0.449s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.88s -Reported 17205 pairwise alignments, 17208 HSPs. -17205 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.034s] -Masking queries... [0.034s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.103s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.059s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.054s] -Building query seed array... [0.016s] -Computing hash join... [0.017s] -Building seed filter... [0.003s] -Searching alignments... [0.049s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.064s] -Building query seed array... [0.022s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.017s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.049s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.048s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.022s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.053s] -Building query seed array... [0.02s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Deallocating buffers... [0.008s] -Computing alignments... [0.454s] -Deallocating reference... [0.005s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.876s -Reported 17102 pairwise alignments, 17107 HSPs. -17102 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.042s] -Masking queries... [0.026s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.018s] -Allocating buffers... [0s] -Loading reference sequences... [0.153s] -Masking reference... [0.106s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.054s] -Building query seed array... [0.012s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.044s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.042s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.009s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.045s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.049s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.039s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Deallocating buffers... [0.01s] -Computing alignments... [0.46s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.785s -Reported 17052 pairwise alignments, 17057 HSPs. -17052 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Bv04_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.036s] -Masking queries... [0.028s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.106s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.051s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.012s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.048s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.037s] -Building query seed array... [0.008s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.037s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.045s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.011s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.041s] -Building query seed array... [0.011s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.028s] -Deallocating buffers... [0.01s] -Computing alignments... [0.422s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.742s -Reported 23370 pairwise alignments, 23380 HSPs. -23370 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.036s] -Masking queries... [0.048s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.013s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.106s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.061s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.059s] -Building query seed array... [0.009s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.045s] -Building query seed array... [0.009s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.044s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.013s] -Computing hash join... [0.008s] -Building seed filter... [0.005s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.049s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.048s] -Building query seed array... [0.01s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.055s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.004s] -Searching alignments... [0.032s] -Deallocating buffers... [0.008s] -Computing alignments... [0.425s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.818s -Reported 23332 pairwise alignments, 23344 HSPs. -23332 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.037s] -Masking queries... [0.03s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.111s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.061s] -Building query seed array... [0.012s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.046s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.048s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Deallocating buffers... [0.008s] -Computing alignments... [0.423s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.842s -Reported 23363 pairwise alignments, 23372 HSPs. -23363 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Usac_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.05s] -Masking queries... [0.032s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.019s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.059s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.056s] -Building query seed array... [0.013s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.084s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.018s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.066s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.064s] -Building query seed array... [0.02s] -Computing hash join... [0.013s] -Building seed filter... [0.005s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.014s] -Computing hash join... [0.008s] -Building seed filter... [0.003s] -Searching alignments... [0.057s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.041s] -Building query seed array... [0.015s] -Computing hash join... [0.009s] -Building seed filter... [0.004s] -Searching alignments... [0.051s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.04s] -Building query seed array... [0.014s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Deallocating buffers... [0.007s] -Computing alignments... [0.748s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.291s -Reported 30410 pairwise alignments, 30414 HSPs. -30410 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.052s] -Masking queries... [0.032s] -Building query seed set... [0.042s] -Algorithm: Double-indexed -Building query histograms... [0.022s] -Allocating buffers... [0s] -Loading reference sequences... [0.146s] -Masking reference... [0.104s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.056s] -Building query seed array... [0.015s] -Computing hash join... [0.019s] -Building seed filter... [0.006s] -Searching alignments... [0.082s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.058s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.021s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.053s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.044s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.045s] -Building query seed array... [0.013s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.05s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.015s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.04s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Deallocating buffers... [0.011s] -Computing alignments... [0.75s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.273s -Reported 30044 pairwise alignments, 30046 HSPs. -30044 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.048s] -Masking queries... [0.033s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.02s] -Allocating buffers... [0s] -Loading reference sequences... [0.147s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.056s] -Building query seed array... [0.012s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.072s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.049s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.063s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.049s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.042s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.055s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.038s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.045s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.052s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.017s] -Computing hash join... [0.009s] -Building seed filter... [0.004s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Deallocating buffers... [0.007s] -Computing alignments... [0.744s] -Deallocating reference... [0.002s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.247s -Reported 30358 pairwise alignments, 30361 HSPs. -30358 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn04_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.015s] -Masking queries... [0.021s] -Building query seed set... [0.022s] -Algorithm: Double-indexed -Building query histograms... [0.013s] -Allocating buffers... [0s] -Loading reference sequences... [0.153s] -Masking reference... [0.109s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.061s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.057s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.006s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.05s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Deallocating buffers... [0.008s] -Computing alignments... [0.232s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.437s -Reported 6507 pairwise alignments, 6514 HSPs. -6507 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.017s] -Masking queries... [0.021s] -Building query seed set... [0.021s] -Algorithm: Double-indexed -Building query histograms... [0.011s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.113s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.011s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.005s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Deallocating buffers... [0.008s] -Computing alignments... [0.241s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.437s -Reported 6501 pairwise alignments, 6504 HSPs. -6501 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.018s] -Masking queries... [0.02s] -Building query seed set... [0.021s] -Algorithm: Double-indexed -Building query histograms... [0.009s] -Allocating buffers... [0s] -Loading reference sequences... [0.145s] -Masking reference... [0.104s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.051s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.063s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.01s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.023s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Deallocating buffers... [0.007s] -Computing alignments... [0.238s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.418s -Reported 6510 pairwise alignments, 6515 HSPs. -6510 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Emar_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.027s] -Masking queries... [0.025s] -Building query seed set... [0.03s] -Algorithm: Double-indexed -Building query histograms... [0.013s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.063s] -Building query seed array... [0.015s] -Computing hash join... [0.015s] -Building seed filter... [0.004s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.021s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Deallocating buffers... [0.008s] -Computing alignments... [0.367s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.744s -Reported 19529 pairwise alignments, 19530 HSPs. -19529 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.022s] -Building query seed set... [0.029s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.106s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.013s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.058s] -Building query seed array... [0.023s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.06s] -Building query seed array... [0.019s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Deallocating buffers... [0.007s] -Computing alignments... [0.375s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.776s -Reported 19648 pairwise alignments, 19649 HSPs. -19648 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.025s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.061s] -Building query seed array... [0.015s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.044s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.048s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Deallocating buffers... [0.007s] -Computing alignments... [0.374s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.739s -Reported 19425 pairwise alignments, 19428 HSPs. -19425 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Rsp1_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.025s] -Masking queries... [0.023s] -Building query seed set... [0.026s] -Algorithm: Double-indexed -Building query histograms... [0.011s] -Allocating buffers... [0s] -Loading reference sequences... [0.159s] -Masking reference... [0.103s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.061s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.058s] -Building query seed array... [0.016s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.018s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.052s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Deallocating buffers... [0.009s] -Computing alignments... [0.284s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.579s -Reported 11921 pairwise alignments, 11926 HSPs. -11921 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.026s] -Masking queries... [0.019s] -Building query seed set... [0.026s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.162s] -Masking reference... [0.108s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.06s] -Building query seed array... [0.015s] -Computing hash join... [0.021s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.021s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.045s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.017s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Deallocating buffers... [0.01s] -Computing alignments... [0.284s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.578s -Reported 11920 pairwise alignments, 11925 HSPs. -11920 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.023s] -Masking queries... [0.023s] -Building query seed set... [0.026s] -Algorithm: Double-indexed -Building query histograms... [0.012s] -Allocating buffers... [0s] -Loading reference sequences... [0.16s] -Masking reference... [0.114s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.07s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.063s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.051s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Deallocating buffers... [0.008s] -Computing alignments... [0.285s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.562s -Reported 11928 pairwise alignments, 11933 HSPs. -11928 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Sspa_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.022s] -Masking queries... [0.023s] -Building query seed set... [0.024s] -Algorithm: Double-indexed -Building query histograms... [0.011s] -Allocating buffers... [0s] -Loading reference sequences... [0.155s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.015s] -Computing hash join... [0.017s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.064s] -Building query seed array... [0.017s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.02s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.063s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.056s] -Building query seed array... [0.011s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Deallocating buffers... [0.008s] -Computing alignments... [0.265s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.554s -Reported 8536 pairwise alignments, 8540 HSPs. -8536 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.023s] -Masking queries... [0.024s] -Building query seed set... [0.027s] -Algorithm: Double-indexed -Building query histograms... [0.018s] -Allocating buffers... [0s] -Loading reference sequences... [0.171s] -Masking reference... [0.112s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.045s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.019s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.044s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.048s] -Building query seed array... [0.015s] -Computing hash join... [0.009s] -Building seed filter... [0.006s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.074s] -Building query seed array... [0.021s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.015s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Deallocating buffers... [0.007s] -Computing alignments... [0.266s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.547s -Reported 8521 pairwise alignments, 8526 HSPs. -8521 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0.001s] -Opening the output file... [0s] -Loading query sequences... [0.024s] -Masking queries... [0.023s] -Building query seed set... [0.025s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.154s] -Masking reference... [0.104s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.057s] -Building query seed array... [0.013s] -Computing hash join... [0.014s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.045s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.045s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.01s] -Deallocating buffers... [0.009s] -Computing alignments... [0.276s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.501s -Reported 8540 pairwise alignments, 8546 HSPs. -8540 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Hhir_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.031s] -Masking queries... [0.024s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.16s] -Masking reference... [0.11s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.068s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.02s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.064s] -Building query seed array... [0.024s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.054s] -Building query seed array... [0.023s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.043s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.065s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.022s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Deallocating buffers... [0.008s] -Computing alignments... [0.389s] -Deallocating reference... [0.005s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.831s -Reported 14131 pairwise alignments, 14135 HSPs. -14131 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0.001s] -Opening the output file... [0s] -Loading query sequences... [0.038s] -Masking queries... [0.034s] -Building query seed set... [0.038s] -Algorithm: Double-indexed -Building query histograms... [0.016s] -Allocating buffers... [0s] -Loading reference sequences... [0.176s] -Masking reference... [0.103s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.061s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.065s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.005s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.02s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.058s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Deallocating buffers... [0.008s] -Computing alignments... [0.39s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.849s -Reported 14101 pairwise alignments, 14103 HSPs. -14101 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.033s] -Masking queries... [0.023s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.176s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.059s] -Building query seed array... [0.018s] -Computing hash join... [0.017s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.063s] -Building query seed array... [0.022s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.063s] -Building query seed array... [0.022s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.063s] -Building query seed array... [0.024s] -Computing hash join... [0.012s] -Building seed filter... [0.005s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Deallocating buffers... [0.008s] -Computing alignments... [0.399s] -Deallocating reference... [0.005s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.842s -Reported 14108 pairwise alignments, 14110 HSPs. -14108 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn12_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.026s] -Masking queries... [0.029s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.165s] -Masking reference... [0.114s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.053s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.018s] -Computing hash join... [0.017s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.013s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.066s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.058s] -Building query seed array... [0.022s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.051s] -Building query seed array... [0.017s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.017s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.045s] -Building query seed array... [0.016s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Deallocating buffers... [0.007s] -Computing alignments... [0.35s] -Deallocating reference... [0.002s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.759s -Reported 13993 pairwise alignments, 13999 HSPs. -13993 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.026s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.012s] -Allocating buffers... [0s] -Loading reference sequences... [0.162s] -Masking reference... [0.107s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.061s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.053s] -Building query seed array... [0.015s] -Computing hash join... [0.018s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.063s] -Building query seed array... [0.021s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.017s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Deallocating buffers... [0.007s] -Computing alignments... [0.371s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.711s -Reported 13983 pairwise alignments, 13987 HSPs. -13983 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.023s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.011s] -Allocating buffers... [0s] -Loading reference sequences... [0.156s] -Masking reference... [0.106s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.061s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.019s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.044s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.049s] -Building query seed array... [0.016s] -Computing hash join... [0.013s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.019s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Deallocating buffers... [0.007s] -Computing alignments... [0.367s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.693s -Reported 13981 pairwise alignments, 13986 HSPs. -13981 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn14_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.053s] -Masking queries... [0.038s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.02s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.104s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.059s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.013s] -Computing hash join... [0.019s] -Building seed filter... [0.003s] -Searching alignments... [0.049s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.049s] -Building query seed array... [0.015s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.049s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.04s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.02s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.051s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.036s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Deallocating buffers... [0.008s] -Computing alignments... [0.647s] -Deallocating reference... [0.002s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.04s -Reported 25265 pairwise alignments, 25285 HSPs. -25265 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.059s] -Masking queries... [0.031s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.026s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.104s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.018s] -Computing hash join... [0.016s] -Building seed filter... [0.004s] -Searching alignments... [0.05s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.016s] -Computing hash join... [0.013s] -Building seed filter... [0.004s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.048s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.043s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.044s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.041s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.024s] -Deallocating buffers... [0.007s] -Computing alignments... [0.666s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.084s -Reported 25226 pairwise alignments, 25252 HSPs. -25226 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.057s] -Masking queries... [0.031s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.024s] -Allocating buffers... [0s] -Loading reference sequences... [0.15s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.065s] -Building query seed array... [0.021s] -Computing hash join... [0.02s] -Building seed filter... [0.003s] -Searching alignments... [0.051s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.038s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.045s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.044s] -Building query seed array... [0.014s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.016s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.041s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Deallocating buffers... [0.007s] -Computing alignments... [0.668s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.088s -Reported 25233 pairwise alignments, 25260 HSPs. -25233 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Gl02_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.034s] -Masking queries... [0.027s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.022s] -Allocating buffers... [0s] -Loading reference sequences... [0.158s] -Masking reference... [0.11s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.053s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.06s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.039s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.048s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.051s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.039s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Deallocating buffers... [0.006s] -Computing alignments... [0.45s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.76s -Reported 17375 pairwise alignments, 17379 HSPs. -17375 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.037s] -Masking queries... [0.024s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.059s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.061s] -Building query seed array... [0.011s] -Computing hash join... [0.017s] -Building seed filter... [0.003s] -Searching alignments... [0.048s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.014s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.051s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.039s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.042s] -Building query seed array... [0.009s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.042s] -Building query seed array... [0.011s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.041s] -Building query seed array... [0.01s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Deallocating buffers... [0.008s] -Computing alignments... [0.465s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.773s -Reported 17358 pairwise alignments, 17365 HSPs. -17358 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.035s] -Masking queries... [0.025s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.017s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.112s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.061s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.055s] -Building query seed array... [0.013s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.013s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.012s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.022s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.055s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.009s] -Computing alignments... [0.47s] -Deallocating reference... [0.002s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.846s -Reported 17328 pairwise alignments, 17333 HSPs. -17328 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Bv05_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.027s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.106s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.069s] -Building query seed array... [0.017s] -Computing hash join... [0.016s] -Building seed filter... [0.004s] -Searching alignments... [0.046s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.018s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.021s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.053s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.049s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.048s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.017s] -Computing hash join... [0.01s] -Building seed filter... [0.005s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.053s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Deallocating buffers... [0.007s] -Computing alignments... [0.389s] -Deallocating reference... [0.005s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.774s -Reported 17843 pairwise alignments, 17846 HSPs. -17843 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.023s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.153s] -Masking reference... [0.105s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.058s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.065s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.02s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.049s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.051s] -Building query seed array... [0.02s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.048s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.016s] -Deallocating buffers... [0.006s] -Computing alignments... [0.394s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.719s -Reported 17817 pairwise alignments, 17820 HSPs. -17817 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.036s] -Masking queries... [0.029s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.016s] -Allocating buffers... [0s] -Loading reference sequences... [0.161s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.054s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.057s] -Building query seed array... [0.015s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.068s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.02s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.022s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.051s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.059s] -Building query seed array... [0.026s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.021s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.058s] -Building query seed array... [0.021s] -Computing hash join... [0.013s] -Building seed filter... [0.004s] -Searching alignments... [0.019s] -Deallocating buffers... [0.008s] -Computing alignments... [0.394s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.838s -Reported 17794 pairwise alignments, 17797 HSPs. -17794 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Bv01_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.01s] -Masking queries... [0.018s] -Building query seed set... [0.012s] -Algorithm: Double-indexed -Building query histograms... [0.009s] -Allocating buffers... [0s] -Loading reference sequences... [0.155s] -Masking reference... [0.122s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.066s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.056s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.058s] -Building query seed array... [0.011s] -Computing hash join... [0.013s] -Building seed filter... [0.006s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.01s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.009s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.046s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.007s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.007s] -Deallocating buffers... [0.007s] -Computing alignments... [0.177s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.345s -Reported 4888 pairwise alignments, 4891 HSPs. -4888 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.01s] -Masking queries... [0.016s] -Building query seed set... [0.011s] -Algorithm: Double-indexed -Building query histograms... [0.005s] -Allocating buffers... [0s] -Loading reference sequences... [0.163s] -Masking reference... [0.126s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.063s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.063s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.012s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.016s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.012s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.014s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.011s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.007s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.008s] -Deallocating buffers... [0.007s] -Computing alignments... [0.176s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.367s -Reported 4897 pairwise alignments, 4900 HSPs. -4897 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.018s] -Masking queries... [0.018s] -Building query seed set... [0.012s] -Algorithm: Double-indexed -Building query histograms... [0.005s] -Allocating buffers... [0s] -Loading reference sequences... [0.155s] -Masking reference... [0.114s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.055s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.057s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.056s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.01s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.012s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.011s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.012s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.009s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.053s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.013s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.007s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.051s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.007s] -Deallocating buffers... [0.009s] -Computing alignments... [0.175s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.345s -Reported 4885 pairwise alignments, 4889 HSPs. -4885 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Slin_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.046s] -Masking queries... [0.035s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.022s] -Allocating buffers... [0s] -Loading reference sequences... [0.156s] -Masking reference... [0.112s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.06s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.058s] -Building query seed array... [0.016s] -Computing hash join... [0.013s] -Building seed filter... [0.004s] -Searching alignments... [0.069s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.067s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.016s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.051s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.046s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.045s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.044s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.039s] -Building query seed array... [0.013s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Deallocating buffers... [0.011s] -Computing alignments... [0.661s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.164s -Reported 26876 pairwise alignments, 26884 HSPs. -26876 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.06s] -Masking queries... [0.035s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.021s] -Allocating buffers... [0s] -Loading reference sequences... [0.148s] -Masking reference... [0.107s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.058s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.067s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.049s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.066s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.052s] -Building query seed array... [0.014s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.041s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.046s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.046s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.046s] -Building query seed array... [0.017s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.051s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.004s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.036s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Deallocating buffers... [0.007s] -Computing alignments... [0.68s] -Deallocating reference... [0.002s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.156s -Reported 26862 pairwise alignments, 26870 HSPs. -26862 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.054s] -Masking queries... [0.031s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.02s] -Allocating buffers... [0s] -Loading reference sequences... [0.157s] -Masking reference... [0.104s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.065s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.066s] -Building query seed array... [0.015s] -Computing hash join... [0.013s] -Building seed filter... [0.004s] -Searching alignments... [0.077s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.067s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.051s] -Building query seed array... [0.018s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.042s] -Building query seed array... [0.014s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.047s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.046s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.044s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.046s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.004s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.042s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Deallocating buffers... [0.01s] -Computing alignments... [0.671s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.192s -Reported 26880 pairwise alignments, 26889 HSPs. -26880 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Gl03_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.04s] -Masking queries... [0.032s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.02s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.113s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.058s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.023s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.063s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.058s] -Building query seed array... [0.021s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.051s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.019s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.038s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.022s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.051s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.049s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.02s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.022s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.048s] -Building query seed array... [0.021s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.029s] -Deallocating buffers... [0.008s] -Computing alignments... [0.644s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.178s -Reported 24415 pairwise alignments, 24421 HSPs. -24415 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.059s] -Masking queries... [0.03s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.018s] -Allocating buffers... [0s] -Loading reference sequences... [0.156s] -Masking reference... [0.106s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.062s] -Building query seed array... [0.014s] -Computing hash join... [0.016s] -Building seed filter... [0.003s] -Searching alignments... [0.066s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.051s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.051s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.013s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.052s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.045s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.043s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.017s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.016s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Deallocating buffers... [0.008s] -Computing alignments... [0.654s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.161s -Reported 24409 pairwise alignments, 24417 HSPs. -24409 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.059s] -Masking queries... [0.029s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.02s] -Allocating buffers... [0s] -Loading reference sequences... [0.151s] -Masking reference... [0.106s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.06s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.065s] -Building query seed array... [0.019s] -Computing hash join... [0.013s] -Building seed filter... [0.006s] -Searching alignments... [0.059s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.051s] -Building query seed array... [0.013s] -Computing hash join... [0.013s] -Building seed filter... [0.005s] -Searching alignments... [0.058s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.013s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.034s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.039s] -Building query seed array... [0.01s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.05s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.043s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.047s] -Building query seed array... [0.013s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.047s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.037s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.012s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Deallocating buffers... [0.008s] -Computing alignments... [0.643s] -Deallocating reference... [0.005s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.112s -Reported 24403 pairwise alignments, 24408 HSPs. -24403 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn09_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.03s] -Masking queries... [0.029s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.147s] -Masking reference... [0.115s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.065s] -Building query seed array... [0.018s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.059s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.015s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.051s] -Building query seed array... [0.018s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.049s] -Building query seed array... [0.019s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.018s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.044s] -Building query seed array... [0.016s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.019s] -Deallocating buffers... [0.009s] -Computing alignments... [0.42s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.79s -Reported 15965 pairwise alignments, 15969 HSPs. -15965 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13 -Opening the database... [0.002s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.037s] -Masking queries... [0.024s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.013s] -Allocating buffers... [0s] -Loading reference sequences... [0.149s] -Masking reference... [0.107s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.065s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.011s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.036s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.047s] -Building query seed array... [0.011s] -Computing hash join... [0.009s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.043s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.042s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.054s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.004s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.05s] -Building query seed array... [0.015s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.041s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Deallocating buffers... [0.009s] -Computing alignments... [0.428s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.723s -Reported 15949 pairwise alignments, 15952 HSPs. -15949 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13 -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.033s] -Masking queries... [0.025s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.017s] -Allocating buffers... [0s] -Loading reference sequences... [0.144s] -Masking reference... [0.117s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.063s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.068s] -Building query seed array... [0.012s] -Computing hash join... [0.015s] -Building seed filter... [0.003s] -Searching alignments... [0.048s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.058s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.058s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.033s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.052s] -Building query seed array... [0.008s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.05s] -Building query seed array... [0.016s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.032s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.055s] -Building query seed array... [0.014s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.046s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Deallocating buffers... [0.008s] -Computing alignments... [0.414s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.797s -Reported 15941 pairwise alignments, 15945 HSPs. -15941 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Nn13_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13 Folder - - -Next Script is: 5_GCodeTranslate.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.005s] -Masking queries... [0.01s] -Building query seed set... [0.005s] -Algorithm: Double-indexed -Building query histograms... [0.002s] -Allocating buffers... [0s] -Loading reference sequences... [0.153s] -Masking reference... [0.104s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.056s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.065s] -Building query seed array... [0.011s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.065s] -Building query seed array... [0.009s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.013s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.001s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.006s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.009s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.003s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.061s] -Building query seed array... [0.01s] -Computing hash join... [0.011s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.013s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.014s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Deallocating buffers... [0.007s] -Computing alignments... [0.042s] -Deallocating reference... [0.008s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.11s -Reported 706 pairwise alignments, 706 HSPs. -706 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.002s] -Masking queries... [0.012s] -Building query seed set... [0.004s] -Algorithm: Double-indexed -Building query histograms... [0.003s] -Allocating buffers... [0s] -Loading reference sequences... [0.152s] -Masking reference... [0.108s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.057s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.061s] -Building query seed array... [0.011s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.057s] -Building query seed array... [0.01s] -Computing hash join... [0.015s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.057s] -Building query seed array... [0.011s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.001s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.05s] -Building query seed array... [0.008s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.001s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.048s] -Building query seed array... [0.007s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.06s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.001s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.056s] -Building query seed array... [0.01s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.057s] -Building query seed array... [0.009s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.001s] -Deallocating buffers... [0.008s] -Computing alignments... [0.042s] -Deallocating reference... [0.004s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.098s -Reported 700 pairwise alignments, 700 HSPs. -700 queries aligned. -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps -Opening the database... [0.001s] -#Target sequences to report alignments for: 1 -Reference = ../Databases/db_StopFreq/RepEukProts.dmnd -Sequences = 156593 -Letters = 61953133 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.002s] -Masking queries... [0.012s] -Building query seed set... [0.003s] -Algorithm: Double-indexed -Building query histograms... [0.002s] -Allocating buffers... [0s] -Loading reference sequences... [0.152s] -Masking reference... [0.117s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.059s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.064s] -Building query seed array... [0.011s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.055s] -Building query seed array... [0.01s] -Computing hash join... [0.014s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.054s] -Building query seed array... [0.009s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.047s] -Building query seed array... [0.011s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.001s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.047s] -Building query seed array... [0.012s] -Computing hash join... [0.012s] -Building seed filter... [0.007s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.052s] -Building query seed array... [0.01s] -Computing hash join... [0.01s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.053s] -Building query seed array... [0.01s] -Computing hash join... [0.012s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.049s] -Building query seed array... [0.01s] -Computing hash join... [0.013s] -Building seed filter... [0.003s] -Searching alignments... [0.002s] -Deallocating buffers... [0.011s] -Computing alignments... [0.038s] -Deallocating reference... [0.003s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.088s -Reported 709 pairwise alignments, 709 HSPs. -709 queries aligned. -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - -Identifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py - - - -Translating DNA using TAA as the sole STOP codon - - - -Translating DNA using TGA as the sole STOP codon - - - -Translating DNA using TAG as the sole STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TGA as only STOP codon - - - -Writing FASTA files with ORF and Protein sequences with TAG as only STOP codon - - - -Gathering Sequence information from FASTA and TSV files - - -Collecting in-frame stop codon information when TGA is the only STOP - - -Collecting in-frame stop codon information when TAG is the only STOP - - -Collecting in-frame stop codon information when TAA is the only STOP - - -Look for Sr_rh_Atps_WTA_EPU.Renamed_StopCodonStats.tsv in the /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps Folder - - -Next Script is: 5_GCodeTranslate.py - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn02_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn02_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn02_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn02_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn02_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn02 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Gspa_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Gspa_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Gspa_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Gspa_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Gspa_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Gspa Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn06_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn06_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn06_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn06_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn06_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn06 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Bv02_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Bv02_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Bv02_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Bv02_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Bv02_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Bv02 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Hind_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Hind_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Hind_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Hind_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Hind_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Hind Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Nn11_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn11_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn11_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn11_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn11_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn11 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Bv03_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Bv03_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Bv03_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Bv03_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Bv03_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Bv03 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Gsp1_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Gsp1_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Gsp1_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Gsp1_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Gsp1_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Gsp1 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Bv06_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Bv06_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Bv06_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Bv06_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Bv06_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Bv06 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Gl01_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Gl01_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Gl01_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Gl01_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Gl01_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Gl01 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Esca_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Esca_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Esca_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Esca_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Esca_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Esca Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Calb_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Calb_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Calb_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Calb_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Calb_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Calb Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Emac_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Emac_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Emac_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Emac_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Emac_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Emac Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn05_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn05_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn05_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn05_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn05_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn05 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn10_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn10_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn10_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn10_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn10_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn10 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Nn03_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn03_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn03_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn03_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn03_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn03 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Halb_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Halb_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Halb_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Halb_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Halb_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Halb Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Nn08_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn08_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn08_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn08_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn08_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn08 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Tx01_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Tx01_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Tx01_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Tx01_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Tx01_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Tx01 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn07_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn07_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn07_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn07_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn07_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn07 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn01_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn01_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn01_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn01_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn01_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn01 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Bv04_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Bv04_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Bv04_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Bv04_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Bv04_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Bv04 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Usac_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Usac_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Usac_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Usac_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Usac_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Usac Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn04_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn04_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn04_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn04_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn04_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn04 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Emar_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Emar_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Emar_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Emar_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Emar_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Emar Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Rsp1_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Rsp1_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Rsp1_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Rsp1_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Rsp1_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Rsp1 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Sspa_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Sspa_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Sspa_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Sspa_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Sspa_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Sspa Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Hhir_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Hhir_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Hhir_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Hhir_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Hhir_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Hhir Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn12_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn12_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn12_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn12_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn12_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn12 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn14_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn14_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn14_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn14_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn14_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn14 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Gl02_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Gl02_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Gl02_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Gl02_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Gl02_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Gl02 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Bv05_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Bv05_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Bv05_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Bv05_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Bv05_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Bv05 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Bv01_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Bv01_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Bv01_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Bv01_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Bv01_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Bv01 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Slin_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Slin_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Slin_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Slin_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Slin_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Slin Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - - - -Grabbing useful info from the Sr_rh_Gl03_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Gl03_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Gl03_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Gl03_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Gl03_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Gl03 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn09_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn09_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn09_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn09_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn09_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn09 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Nn13_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Nn13_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Nn13_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Nn13_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Nn13_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Nn13 Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) -/gridapps/software/Biopython/1.75-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/Bio/Seq.py:2748: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future. - BiopythonWarning) - - -Grabbing useful info from the Sr_rh_Atps_WTA_EPU.Renamed.fasta Fasta File -and from the Sr_rh_Atps_WTA_EPU.Renamed_allOGCleanresults.tsv OG-Assignment Spreadsheet - - -Extracting ORFs from the transcriptomic data-set - - - - -Translating ORFs from using the Universal genetic code - - -Writing FASTA file with ORF sequences using the Universal genetic code - - -Writing FASTA file with Translated ORF sequences using the Universal genetic code - - -Look for Sr_rh_Atps_WTA_EPU.Renamed_Universal_NTD.ORF.fasta, -Sr_rh_Atps_WTA_EPU.Renamed_Universal_AA.ORF.fasta, and -Sr_rh_Atps_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv, -which are in the Sr_rh_Atps Folder - - -Next Script is: 6_FilterPartials.py in the FinalizeTranscripts Folder -with a copy of the outputs of this script! - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1/Original/Concatenated/Sr_rh_Rsp1.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.024s] -Masking sequences... [0.024s] -Writing sequences... [0.008s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = bab6450592789937ae623d8d5a857e95 -Processed 23164 sequences, 4715295 letters. -Total time = 0.063s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Rsp1/Original/Concatenated/Sr_rh_Rsp1.AA.Concatenated.dmnd -Sequences = 23164 -Letters = 4715295 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.032s] -Masking queries... [0.022s] -Building query seed set... [0.03s] -Algorithm: Double-indexed -Building query histograms... [0.011s] -Allocating buffers... [0s] -Loading reference sequences... [0.014s] -Masking reference... [0.014s] -Initializing temporary storage... [0.008s] -Building reference histograms... [0.011s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.016s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.058s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.018s] -Building query seed array... [0.017s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.051s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.015s] -Building query seed array... [0.021s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.049s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.015s] -Building query seed array... [0.018s] -Computing hash join... [0.004s] -Building seed filter... [0.006s] -Searching alignments... [0.055s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.017s] -Building query seed array... [0.014s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.052s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.02s] -Building query seed array... [0.018s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.049s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.02s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.049s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.023s] -Building query seed array... [0.018s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.049s] -Deallocating buffers... [0.001s] -Computing alignments... [0.529s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.449s -Reported 213997 pairwise alignments, 214009 HSPs. -20278 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Rsp1 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Rsp1 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Rsp1 - - -There were 23164 ORFs originally, with 402 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 23164 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1460 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 3886 Unique ORFs for Sr_rh_Rsp1 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa/Original/Concatenated/Sr_rh_Gspa.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.015s] -Masking sequences... [0.022s] -Writing sequences... [0.005s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = a6c8290dedcc9f8988a2173a11da18c7 -Processed 7105 sequences, 3003718 letters. -Total time = 0.048s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gspa/Original/Concatenated/Sr_rh_Gspa.AA.Concatenated.dmnd -Sequences = 7105 -Letters = 3003718 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.021s] -Masking queries... [0.022s] -Building query seed set... [0.022s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.011s] -Masking reference... [0.012s] -Initializing temporary storage... [0.008s] -Building reference histograms... [0.009s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.012s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.012s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.008s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.011s] -Building query seed array... [0.012s] -Computing hash join... [0.004s] -Building seed filter... [0.007s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.01s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.016s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.012s] -Building query seed array... [0.014s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.011s] -Building query seed array... [0.007s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.01s] -Building query seed array... [0.008s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.016s] -Deallocating buffers... [0s] -Computing alignments... [0.163s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 0.688s -Reported 21465 pairwise alignments, 21479 HSPs. -4188 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Gspa at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Gspa - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Gspa - - -There were 7105 ORFs originally, with 403 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 7105 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 247 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 3885 Unique ORFs for Sr_rh_Gspa - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06/Original/Concatenated/Sr_rh_Bv06.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.025s] -Masking sequences... [0.025s] -Writing sequences... [0.006s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0.001s] -Database hash = 0d69e46f38fb37d85dde5e9893f95811 -Processed 13330 sequences, 3179706 letters. -Total time = 0.064s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv06/Original/Concatenated/Sr_rh_Bv06.AA.Concatenated.dmnd -Sequences = 13330 -Letters = 3179706 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.019s] -Masking queries... [0.02s] -Building query seed set... [0.022s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.01s] -Masking reference... [0.013s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.01s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.016s] -Building query seed array... [0.017s] -Computing hash join... [0.005s] -Building seed filter... [0.004s] -Searching alignments... [0.035s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.011s] -Building query seed array... [0.015s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.011s] -Building query seed array... [0.015s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.011s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.028s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.01s] -Building query seed array... [0.007s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.011s] -Building query seed array... [0.013s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.013s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.013s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.024s] -Deallocating buffers... [0s] -Computing alignments... [0.354s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 0.974s -Reported 118156 pairwise alignments, 118180 HSPs. -10897 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Bv06 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Bv06 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Bv06 - - -There were 13330 ORFs originally, with 247 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 13330 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 708 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 3447 Unique ORFs for Sr_rh_Bv06 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05/Original/Concatenated/Sr_rh_Bv05.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.034s] -Masking sequences... [0.032s] -Writing sequences... [0.01s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0.001s] -Database hash = f232a8887cb0b9a70c7d1734930dc141 -Processed 21731 sequences, 6537985 letters. -Total time = 0.084s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv05/Original/Concatenated/Sr_rh_Bv05.AA.Concatenated.dmnd -Sequences = 21731 -Letters = 6537985 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.046s] -Masking queries... [0.03s] -Building query seed set... [0.037s] -Algorithm: Double-indexed -Building query histograms... [0.016s] -Allocating buffers... [0s] -Loading reference sequences... [0.02s] -Masking reference... [0.019s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.017s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.018s] -Building query seed array... [0.011s] -Computing hash join... [0.005s] -Building seed filter... [0.003s] -Searching alignments... 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[0s] -Total time = 2.041s -Reported 247684 pairwise alignments, 247700 HSPs. -18611 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Bv05 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Bv05 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Bv05 - - -There were 21731 ORFs originally, with 985 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 21731 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1186 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4673 Unique ORFs for Sr_rh_Bv05 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir/Original/Concatenated/Sr_rh_Hhir.AA.Concatenated.fasta -Opening the database file... [0.001s] -Loading sequences... [0.029s] -Masking sequences... [0.025s] -Writing sequences... [0.007s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 428316e31713e49d2d7dce86c739ac6d -Processed 10555 sequences, 4383683 letters. -Total time = 0.067s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hhir/Original/Concatenated/Sr_rh_Hhir.AA.Concatenated.dmnd -Sequences = 10555 -Letters = 4383683 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.021s] -Building query seed set... [0.028s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.011s] -Masking reference... [0.015s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.013s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.015s] -Building query seed array... [0.017s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... 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[0.004s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.016s] -Building query seed array... [0.017s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.013s] -Building query seed array... [0.01s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.03s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.019s] -Building query seed array... [0.018s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Deallocating buffers... [0s] -Computing alignments... [0.348s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 1.045s -Reported 74899 pairwise alignments, 74902 HSPs. -8134 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Hhir at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Hhir - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Hhir - - -There were 10555 ORFs originally, with 539 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 10555 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 276 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 3796 Unique ORFs for Sr_rh_Hhir - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac/Original/Concatenated/Sr_rh_Usac.AA.Concatenated.fasta -Opening the database file... [0.003s] -Loading sequences... [0.04s] -Masking sequences... [0.03s] -Writing sequences... [0.01s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 8b58851e74ea699eb4d51c09aeec1dbf -Processed 28139 sequences, 6273041 letters. -Total time = 0.088s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Usac/Original/Concatenated/Sr_rh_Usac.AA.Concatenated.dmnd -Sequences = 28139 -Letters = 6273041 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.04s] -Masking queries... [0.029s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.019s] -Masking reference... [0.021s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.013s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.02s] -Building query seed array... [0.012s] -Computing hash join... [0.004s] -Building seed filter... [0.006s] -Searching alignments... 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[0.004s] -Searching alignments... [0.054s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.012s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.05s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.009s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.053s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.01s] -Building query seed array... [0.011s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.045s] -Deallocating buffers... [0s] -Computing alignments... [0.662s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 1.57s -Reported 254805 pairwise alignments, 254821 HSPs. -22199 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Usac at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Usac - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Usac - - -There were 28139 ORFs originally, with 552 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 28139 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 2668 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 5891 Unique ORFs for Sr_rh_Usac - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12/Original/Concatenated/Sr_rh_Nn12.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.027s] -Masking sequences... [0.025s] -Writing sequences... [0.008s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = e7d4a4c31fbd8f98b96b01981ecc8606 -Processed 17423 sequences, 5488596 letters. -Total time = 0.067s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn12/Original/Concatenated/Sr_rh_Nn12.AA.Concatenated.dmnd -Sequences = 17423 -Letters = 5488596 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.023s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.012s] -Allocating buffers... [0s] -Loading reference sequences... [0.015s] -Masking reference... [0.018s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.012s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.017s] -Building query seed array... [0.015s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... 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[0.004s] -Searching alignments... [0.046s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.019s] -Building query seed array... [0.019s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.043s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.02s] -Building query seed array... [0.02s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.016s] -Building query seed array... [0.018s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.044s] -Deallocating buffers... [0.001s] -Computing alignments... [0.559s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 1.461s -Reported 130509 pairwise alignments, 130513 HSPs. -13655 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn12 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn12 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn12 - - -There were 17423 ORFs originally, with 714 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 17423 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1428 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4918 Unique ORFs for Sr_rh_Nn12 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11/Original/Concatenated/Sr_rh_Nn11.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.025s] -Masking sequences... [0.027s] -Writing sequences... [0.009s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = ce23face356f3db46ecedaa798ad5aef -Processed 16742 sequences, 5190604 letters. -Total time = 0.068s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn11/Original/Concatenated/Sr_rh_Nn11.AA.Concatenated.dmnd -Sequences = 16742 -Letters = 5190604 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.026s] -Masking queries... [0.023s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.015s] -Masking reference... [0.016s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.011s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.019s] -Building query seed array... [0.014s] -Computing hash join... [0.005s] -Building seed filter... [0.004s] -Searching alignments... 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[0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.293s -Reported 118397 pairwise alignments, 118399 HSPs. -12869 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn11 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn11 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn11 - - -There were 16742 ORFs originally, with 605 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 16742 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1489 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4851 Unique ORFs for Sr_rh_Nn11 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac/Original/Concatenated/Sr_rh_Emac.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.019s] -Masking sequences... [0.021s] -Writing sequences... [0.005s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0.001s] -Database hash = 64cf2a04524c8e16fd6656e71370d508 -Processed 9237 sequences, 3633229 letters. -Total time = 0.051s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emac/Original/Concatenated/Sr_rh_Emac.AA.Concatenated.dmnd -Sequences = 9237 -Letters = 3633229 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.023s] -Masking queries... [0.021s] -Building query seed set... [0.022s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.009s] -Masking reference... [0.013s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.009s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.014s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... 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[0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 0.903s -Reported 63591 pairwise alignments, 63591 HSPs. -7137 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Emac at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Emac - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Emac - - -There were 9237 ORFs originally, with 832 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 9237 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 279 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 3032 Unique ORFs for Sr_rh_Emac - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07/Original/Concatenated/Sr_rh_Nn07.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.039s] -Masking sequences... [0.032s] -Writing sequences... [0.012s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0.001s] -Database hash = 8244245367c3ffdbc45bb090b15f7b05 -Processed 23977 sequences, 7324212 letters. -Total time = 0.092s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn07/Original/Concatenated/Sr_rh_Nn07.AA.Concatenated.dmnd -Sequences = 23977 -Letters = 7324212 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.05s] -Masking queries... [0.027s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.017s] -Allocating buffers... [0s] -Loading reference sequences... [0.022s] -Masking reference... [0.022s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.018s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.018s] -Building query seed array... [0.012s] -Computing hash join... [0.005s] -Building seed filter... [0.007s] -Searching alignments... 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[0.003s] -Searching alignments... [0.161s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.019s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.126s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.018s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.136s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.015s] -Building query seed array... [0.01s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.128s] -Deallocating buffers... [0.001s] -Computing alignments... [1.08s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... 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[0s] -Total time = 2.825s -Reported 245593 pairwise alignments, 245597 HSPs. -19882 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn07 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn07 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn07 - - -There were 23977 ORFs originally, with 2660 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 23977 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1830 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 5510 Unique ORFs for Sr_rh_Nn07 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13/Original/Concatenated/Sr_rh_Nn13.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.033s] -Masking sequences... [0.028s] -Writing sequences... [0.009s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 6284262dc2b368563c66830b2de682fe -Processed 19632 sequences, 6226238 letters. -Total time = 0.077s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn13/Original/Concatenated/Sr_rh_Nn13.AA.Concatenated.dmnd -Sequences = 19632 -Letters = 6226238 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.033s] -Masking queries... [0.027s] -Building query seed set... [0.031s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.016s] -Masking reference... [0.019s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.013s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.017s] -Building query seed array... [0.014s] -Computing hash join... [0.006s] -Building seed filter... [0.004s] -Searching alignments... 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[0.003s] -Searching alignments... [0.066s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.01s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.063s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.011s] -Building query seed array... [0.011s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.059s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.009s] -Building query seed array... [0.009s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.059s] -Deallocating buffers... [0s] -Computing alignments... [0.711s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 1.702s -Reported 167005 pairwise alignments, 167007 HSPs. -15814 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn13 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn13 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn13 - - -There were 19632 ORFs originally, with 1170 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 19632 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1617 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 5105 Unique ORFs for Sr_rh_Nn13 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind/Original/Concatenated/Sr_rh_Hind.AA.Concatenated.fasta -Opening the database file... [0.001s] -Loading sequences... [0.023s] -Masking sequences... [0.024s] -Writing sequences... [0.007s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 31071ed620ecc09074d6eef75556a9f9 -Processed 10997 sequences, 4801737 letters. -Total time = 0.059s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Hind/Original/Concatenated/Sr_rh_Hind.AA.Concatenated.dmnd -Sequences = 10997 -Letters = 4801737 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.026s] -Masking queries... [0.021s] -Building query seed set... [0.031s] -Algorithm: Double-indexed -Building query histograms... [0.013s] -Allocating buffers... [0s] -Loading reference sequences... [0.012s] -Masking reference... [0.016s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.009s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.016s] -Building query seed array... [0.014s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... 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[0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.014s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.046s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.015s] -Building query seed array... [0.018s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.016s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.039s] -Deallocating buffers... [0s] -Computing alignments... [0.412s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 1.221s -Reported 85965 pairwise alignments, 86115 HSPs. -9226 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Hind at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Hind - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Hind - - -There were 10997 ORFs originally, with 1346 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 10997 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 307 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 2768 Unique ORFs for Sr_rh_Hind - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin/Original/Concatenated/Sr_rh_Slin.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.016s] -Masking sequences... [0.016s] -Writing sequences... [0.003s] -Hashing sequences... [0s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = eb21f94236c55caa57cea789977257e5 -Processed 5832 sequences, 1943459 letters. -Total time = 0.04s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Slin/Original/Concatenated/Sr_rh_Slin.AA.Concatenated.dmnd -Sequences = 5832 -Letters = 1943459 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.017s] -Masking queries... [0.015s] -Building query seed set... [0.012s] -Algorithm: Double-indexed -Building query histograms... [0.005s] -Allocating buffers... [0s] -Loading reference sequences... [0.007s] -Masking reference... [0.009s] -Initializing temporary storage... [0.008s] -Building reference histograms... [0.004s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.013s] -Building query seed array... [0.014s] -Computing hash join... [0.003s] -Building seed filter... [0.005s] -Searching alignments... [0.029s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.01s] -Building query seed array... [0.011s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.009s] -Building query seed array... [0.011s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.019s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.012s] -Building query seed array... [0.008s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.017s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.008s] -Building query seed array... [0.008s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.018s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.009s] -Building query seed array... [0.009s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.015s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.009s] -Building query seed array... [0.01s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.011s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.005s] -Searching alignments... [0.015s] -Deallocating buffers... [0s] -Computing alignments... [0.144s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 0.621s -Reported 32543 pairwise alignments, 32545 HSPs. -3816 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Slin at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Slin - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Slin - - -There were 5832 ORFs originally, with 441 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 5832 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 279 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 2566 Unique ORFs for Sr_rh_Slin - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps/Original/Concatenated/Sr_rh_Atps.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.002s] -Masking sequences... [0.011s] -Writing sequences... [0s] -Hashing sequences... [0s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 032e18933d35f2dcdbd89f8365a0e29b -Processed 1572 sequences, 304954 letters. -Total time = 0.018s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Atps/Original/Concatenated/Sr_rh_Atps.AA.Concatenated.dmnd -Sequences = 1572 -Letters = 304954 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.002s] -Masking queries... [0.009s] -Building query seed set... [0.003s] -Algorithm: Double-indexed -Building query histograms... [0.003s] -Allocating buffers... [0s] -Loading reference sequences... [0.001s] -Masking reference... [0.004s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.003s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.014s] -Building query seed array... [0.014s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.007s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.011s] -Building query seed array... [0.007s] -Computing hash join... [0.002s] -Building seed filter... [0.005s] -Searching alignments... [0.005s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.007s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Building seed filter... [0.003s] -Searching alignments... [0.005s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.007s] -Building query seed array... [0.006s] -Computing hash join... [0.002s] -Building seed filter... [0.005s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.013s] -Building query seed array... [0.006s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.005s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.013s] -Building query seed array... [0.007s] -Computing hash join... [0.001s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.007s] -Building query seed array... [0.006s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.006s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Deallocating buffers... [0s] -Computing alignments... [0.031s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 0.307s -Reported 2855 pairwise alignments, 2855 HSPs. -490 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Atps at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Atps - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Atps - - -There were 1572 ORFs originally, with 39 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 1572 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 119 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 1065 Unique ORFs for Sr_rh_Atps - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb/Original/Concatenated/Sr_rh_Calb.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.026s] -Masking sequences... [0.024s] -Writing sequences... [0.009s] -Hashing sequences... [0.003s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = c31e6238b80f6551ff9fba31e8253bf7 -Processed 10532 sequences, 3924177 letters. -Total time = 0.067s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Calb/Original/Concatenated/Sr_rh_Calb.AA.Concatenated.dmnd -Sequences = 10532 -Letters = 3924177 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.022s] -Masking queries... [0.024s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.01s] -Masking reference... [0.013s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.009s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.017s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.012s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.012s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.024s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.011s] -Building query seed array... [0.014s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.012s] -Building query seed array... [0.014s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.012s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.013s] -Building query seed array... [0.016s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.011s] -Building query seed array... [0.013s] -Computing hash join... [0.002s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Deallocating buffers... [0s] -Computing alignments... [0.38s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.027s -Reported 89461 pairwise alignments, 89467 HSPs. -8205 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Calb at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Calb - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Calb - - -There were 10532 ORFs originally, with 339 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 10532 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 350 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 3460 Unique ORFs for Sr_rh_Calb - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1/Original/Concatenated/Sr_rh_Gsp1.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.018s] -Masking sequences... [0.021s] -Writing sequences... [0.005s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = e29604468b49ff25602af34bf175d55b -Processed 9075 sequences, 3395806 letters. -Total time = 0.049s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gsp1/Original/Concatenated/Sr_rh_Gsp1.AA.Concatenated.dmnd -Sequences = 9075 -Letters = 3395806 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.018s] -Masking queries... [0.021s] -Building query seed set... [0.023s] -Algorithm: Double-indexed -Building query histograms... [0.009s] -Allocating buffers... [0s] -Loading reference sequences... [0.01s] -Masking reference... [0.013s] -Initializing temporary storage... [0.008s] -Building reference histograms... [0.006s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.014s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.005s] -Searching alignments... [0.031s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.015s] -Building query seed array... [0.02s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.027s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.015s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.011s] -Building query seed array... [0.008s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.013s] -Building query seed array... [0.009s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.012s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.012s] -Building query seed array... [0.014s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.02s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.01s] -Building query seed array... [0.007s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.023s] -Deallocating buffers... [0s] -Computing alignments... [0.272s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 0.859s -Reported 57494 pairwise alignments, 57495 HSPs. -6675 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Gsp1 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Gsp1 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Gsp1 - - -There were 9075 ORFs originally, with 410 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 9075 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 386 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 3393 Unique ORFs for Sr_rh_Gsp1 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08/Original/Concatenated/Sr_rh_Nn08.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.022s] -Masking sequences... [0.026s] -Writing sequences... [0.007s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 5aaed5bdda45faa3943131907b7845d5 -Processed 15500 sequences, 3990841 letters. -Total time = 0.062s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn08/Original/Concatenated/Sr_rh_Nn08.AA.Concatenated.dmnd -Sequences = 15500 -Letters = 3990841 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.024s] -Building query seed set... [0.031s] -Algorithm: Double-indexed -Building query histograms... [0.017s] -Allocating buffers... [0s] -Loading reference sequences... [0.015s] -Masking reference... [0.015s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.009s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.014s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.158s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.023s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.124s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.022s] -Building query seed array... [0.016s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.113s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.016s] -Building query seed array... [0.017s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.12s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.019s] -Building query seed array... [0.018s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.109s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.017s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.102s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.015s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.121s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.021s] -Building query seed array... [0.012s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.101s] -Deallocating buffers... [0s] -Computing alignments... [0.615s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.065s -Reported 166114 pairwise alignments, 166116 HSPs. -12320 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn08 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn08 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn08 - - -There were 15500 ORFs originally, with 2616 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 15500 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1059 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4023 Unique ORFs for Sr_rh_Nn08 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04/Original/Concatenated/Sr_rh_Nn04.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.048s] -Masking sequences... [0.037s] -Writing sequences... [0.015s] -Hashing sequences... [0.004s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 95f78e5fe98e9036e94658c2ba4f58da -Processed 36674 sequences, 9173466 letters. -Total time = 0.11s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn04/Original/Concatenated/Sr_rh_Nn04.AA.Concatenated.dmnd -Sequences = 36674 -Letters = 9173466 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.049s] -Masking queries... [0.034s] -Building query seed set... [0.039s] -Algorithm: Double-indexed -Building query histograms... [0.021s] -Allocating buffers... [0s] -Loading reference sequences... [0.025s] -Masking reference... [0.029s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.018s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.019s] -Building query seed array... [0.019s] -Computing hash join... [0.006s] -Building seed filter... [0.004s] -Searching alignments... 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[0.004s] -Searching alignments... [0.347s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.023s] -Building query seed array... [0.016s] -Computing hash join... [0.005s] -Building seed filter... [0.004s] -Searching alignments... [0.298s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.026s] -Building query seed array... [0.02s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.307s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.02s] -Building query seed array... [0.011s] -Computing hash join... [0.005s] -Building seed filter... [0.003s] -Searching alignments... [0.29s] -Deallocating buffers... [0.002s] -Computing alignments... [1.939s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 5.355s -Reported 475363 pairwise alignments, 475381 HSPs. -31089 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn04 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn04 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn04 - - -There were 36674 ORFs originally, with 7073 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 36674 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 3043 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 6419 Unique ORFs for Sr_rh_Nn04 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01/Original/Concatenated/Sr_rh_Bv01.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.027s] -Masking sequences... [0.027s] -Writing sequences... [0.009s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 32762a5b753a4aa6704d518df14f98b0 -Processed 22250 sequences, 5423683 letters. -Total time = 0.07s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv01/Original/Concatenated/Sr_rh_Bv01.AA.Concatenated.dmnd -Sequences = 22250 -Letters = 5423683 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.026s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.017s] -Masking reference... [0.016s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.011s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.02s] -Building query seed array... [0.018s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... 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[0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.017s] -Building query seed array... [0.02s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.014s] -Building query seed array... [0.017s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.045s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.014s] -Building query seed array... [0.016s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.044s] -Deallocating buffers... [0s] -Computing alignments... [0.694s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... 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[0s] -Total time = 1.582s -Reported 210419 pairwise alignments, 210421 HSPs. -17900 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Bv01 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Bv01 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Bv01 - - -There were 22250 ORFs originally, with 925 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 22250 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1761 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 5198 Unique ORFs for Sr_rh_Bv01 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05/Original/Concatenated/Sr_rh_Nn05.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.026s] -Masking sequences... [0.031s] -Writing sequences... [0.009s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 53344b07d607f88908ffa47877c05848 -Processed 17028 sequences, 5371066 letters. -Total time = 0.073s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn05/Original/Concatenated/Sr_rh_Nn05.AA.Concatenated.dmnd -Sequences = 17028 -Letters = 5371066 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.028s] -Masking queries... [0.026s] -Building query seed set... [0.032s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.013s] -Masking reference... [0.019s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.017s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.015s] -Building query seed array... [0.013s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... 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[0.004s] -Searching alignments... [0.059s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.018s] -Building query seed array... [0.019s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.053s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.018s] -Building query seed array... [0.021s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.058s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.018s] -Building query seed array... [0.02s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.053s] -Deallocating buffers... [0s] -Computing alignments... [0.573s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 1.605s -Reported 136247 pairwise alignments, 136251 HSPs. -13401 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn05 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn05 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn05 - - -There were 17028 ORFs originally, with 1026 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 17028 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1409 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4799 Unique ORFs for Sr_rh_Nn05 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03/Original/Concatenated/Sr_rh_Gl03.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.052s] -Masking sequences... [0.051s] -Writing sequences... [0.016s] -Hashing sequences... [0.003s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 8c5853401a6b05601e71e4bc98b8ba39 -Processed 32752 sequences, 10207231 letters. -Total time = 0.128s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl03/Original/Concatenated/Sr_rh_Gl03.AA.Concatenated.dmnd -Sequences = 32752 -Letters = 10207231 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.059s] -Masking queries... [0.036s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.022s] -Allocating buffers... [0s] -Loading reference sequences... [0.028s] -Masking reference... [0.025s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.019s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.026s] -Building query seed array... [0.016s] -Computing hash join... [0.007s] -Building seed filter... [0.004s] -Searching alignments... 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[0.004s] -Searching alignments... [0.074s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.019s] -Building query seed array... [0.019s] -Computing hash join... [0.005s] -Building seed filter... [0.004s] -Searching alignments... [0.07s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.022s] -Building query seed array... [0.018s] -Computing hash join... [0.005s] -Building seed filter... [0.005s] -Searching alignments... [0.074s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.014s] -Building query seed array... [0.014s] -Computing hash join... [0.005s] -Building seed filter... [0.004s] -Searching alignments... [0.067s] -Deallocating buffers... [0.001s] -Computing alignments... [1.422s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... 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[0s] -Total time = 2.681s -Reported 371577 pairwise alignments, 371643 HSPs. -30596 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Gl03 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Gl03 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Gl03 - - -There were 32752 ORFs originally, with 835 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 32752 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1335 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4863 Unique ORFs for Sr_rh_Gl03 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar/Original/Concatenated/Sr_rh_Emar.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.016s] -Masking sequences... [0.022s] -Writing sequences... [0.005s] -Hashing sequences... [0s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 0377bff5727d8ea0665197857dd36934 -Processed 7943 sequences, 3401675 letters. -Total time = 0.048s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Emar/Original/Concatenated/Sr_rh_Emar.AA.Concatenated.dmnd -Sequences = 7943 -Letters = 3401675 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.017s] -Masking queries... [0.019s] -Building query seed set... [0.021s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.009s] -Masking reference... [0.017s] -Initializing temporary storage... [0.008s] -Building reference histograms... [0.009s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.017s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... 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[0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 0.847s -Reported 45208 pairwise alignments, 45211 HSPs. -5967 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Emar at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Emar - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Emar - - -There were 7943 ORFs originally, with 828 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 7943 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 195 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 3036 Unique ORFs for Sr_rh_Emar - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02/Original/Concatenated/Sr_rh_Nn02.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.028s] -Masking sequences... [0.026s] -Writing sequences... [0.009s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = fafb09591ab6392c934e41fce1e5cc78 -Processed 18186 sequences, 5834132 letters. -Total time = 0.07s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn02/Original/Concatenated/Sr_rh_Nn02.AA.Concatenated.dmnd -Sequences = 18186 -Letters = 5834132 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.024s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.013s] -Allocating buffers... [0s] -Loading reference sequences... [0.015s] -Masking reference... [0.017s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.01s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.021s] -Building query seed array... [0.018s] -Computing hash join... [0.005s] -Building seed filter... [0.003s] -Searching alignments... 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[0.004s] -Searching alignments... [0.142s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.027s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.12s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.023s] -Building query seed array... [0.017s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.16s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.025s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.147s] -Deallocating buffers... [0.001s] -Computing alignments... [0.831s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.506s -Reported 179318 pairwise alignments, 179321 HSPs. -14504 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn02 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn02 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn02 - - -There were 18186 ORFs originally, with 1966 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 18186 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1352 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4670 Unique ORFs for Sr_rh_Nn02 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10/Original/Concatenated/Sr_rh_Nn10.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.035s] -Masking sequences... [0.032s] -Writing sequences... [0.01s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 2c8f05bd448e81fa11fb1f390a5a1b16 -Processed 20167 sequences, 6887392 letters. -Total time = 0.085s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn10/Original/Concatenated/Sr_rh_Nn10.AA.Concatenated.dmnd -Sequences = 20167 -Letters = 6887392 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.04s] -Masking queries... [0.025s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.019s] -Allocating buffers... [0s] -Loading reference sequences... [0.022s] -Masking reference... [0.021s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.015s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.02s] -Building query seed array... [0.011s] -Computing hash join... [0.004s] -Building seed filter... [0.005s] -Searching alignments... [0.213s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.021s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.171s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.017s] -Building query seed array... [0.015s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.164s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.017s] -Building query seed array... [0.009s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.156s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.014s] -Building query seed array... [0.01s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.151s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.014s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.128s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.015s] -Building query seed array... [0.014s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.174s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.019s] -Building query seed array... [0.011s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.14s] -Deallocating buffers... [0.001s] -Computing alignments... [1.167s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.983s -Reported 236210 pairwise alignments, 236216 HSPs. -16852 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn10 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn10 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn10 - - -There were 20167 ORFs originally, with 2853 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 20167 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1214 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4580 Unique ORFs for Sr_rh_Nn10 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03/Original/Concatenated/Sr_rh_Nn03.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.035s] -Masking sequences... [0.028s] -Writing sequences... [0.009s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 103564f9e7dd2f1f2bec1ec8db24c811 -Processed 17953 sequences, 5742700 letters. -Total time = 0.079s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn03/Original/Concatenated/Sr_rh_Nn03.AA.Concatenated.dmnd -Sequences = 17953 -Letters = 5742700 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.031s] -Masking queries... [0.026s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.013s] -Allocating buffers... [0s] -Loading reference sequences... [0.016s] -Masking reference... [0.017s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.012s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.022s] -Building query seed array... [0.017s] -Computing hash join... [0.005s] -Building seed filter... [0.003s] -Searching alignments... 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[0.004s] -Searching alignments... [0.065s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.016s] -Building query seed array... [0.017s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.061s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.018s] -Building query seed array... [0.02s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.075s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.021s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.068s] -Deallocating buffers... [0s] -Computing alignments... [0.684s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 1.832s -Reported 154410 pairwise alignments, 154413 HSPs. -14138 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn03 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn03 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn03 - - -There were 17953 ORFs originally, with 1458 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 17953 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1522 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4771 Unique ORFs for Sr_rh_Nn03 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06/Original/Concatenated/Sr_rh_Nn06.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.032s] -Masking sequences... [0.029s] -Writing sequences... [0.01s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 9d688130f29a63e4d67352cdb9f99ac1 -Processed 19812 sequences, 6063731 letters. -Total time = 0.077s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn06/Original/Concatenated/Sr_rh_Nn06.AA.Concatenated.dmnd -Sequences = 19812 -Letters = 6063731 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.032s] -Masking queries... [0.029s] -Building query seed set... [0.035s] -Algorithm: Double-indexed -Building query histograms... [0.016s] -Allocating buffers... [0s] -Loading reference sequences... [0.02s] -Masking reference... [0.018s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.011s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.017s] -Building query seed array... [0.011s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.139s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.017s] -Building query seed array... [0.01s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.103s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.014s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.102s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.012s] -Building query seed array... [0.012s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.09s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.01s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.107s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.014s] -Building query seed array... [0.01s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.084s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.014s] -Building query seed array... [0.011s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.093s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.012s] -Building query seed array... [0.013s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.081s] -Deallocating buffers... [0s] -Computing alignments... [0.802s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 2.059s -Reported 193966 pairwise alignments, 193972 HSPs. -16000 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn06 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn06 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn06 - - -There were 19812 ORFs originally, with 1949 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 19812 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1501 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4947 Unique ORFs for Sr_rh_Nn06 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02/Original/Concatenated/Sr_rh_Bv02.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.034s] -Masking sequences... [0.029s] -Writing sequences... [0.011s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 96b1fdedb1bc7f9735f8d6a9c060b359 -Processed 24278 sequences, 6856585 letters. -Total time = 0.081s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv02/Original/Concatenated/Sr_rh_Bv02.AA.Concatenated.dmnd -Sequences = 24278 -Letters = 6856585 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.047s] -Masking queries... [0.031s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.02s] -Allocating buffers... [0s] -Loading reference sequences... [0.021s] -Masking reference... [0.02s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.01s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.018s] -Building query seed array... [0.016s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... 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[0.004s] -Searching alignments... [0.066s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.023s] -Building query seed array... [0.02s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.062s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.02s] -Building query seed array... [0.02s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.06s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.018s] -Building query seed array... [0.02s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.058s] -Deallocating buffers... [0.001s] -Computing alignments... [1.001s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.159s -Reported 274535 pairwise alignments, 274572 HSPs. -20473 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Bv02 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Bv02 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Bv02 - - -There were 24278 ORFs originally, with 1366 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 24278 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1535 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 5142 Unique ORFs for Sr_rh_Bv02 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02/Original/Concatenated/Sr_rh_Gl02.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.055s] -Masking sequences... [0.042s] -Writing sequences... [0.017s] -Hashing sequences... [0.003s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 9fd3ebe1fc02a1cc4b69bb7b2be9a35d -Processed 31505 sequences, 11021837 letters. -Total time = 0.123s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl02/Original/Concatenated/Sr_rh_Gl02.AA.Concatenated.dmnd -Sequences = 31505 -Letters = 11021837 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.057s] -Masking queries... [0.034s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.021s] -Allocating buffers... [0s] -Loading reference sequences... [0.028s] -Masking reference... [0.028s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.02s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.026s] -Building query seed array... [0.019s] -Computing hash join... [0.008s] -Building seed filter... [0.003s] -Searching alignments... 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[0.004s] -Searching alignments... [0.081s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.016s] -Building query seed array... [0.013s] -Computing hash join... [0.005s] -Building seed filter... [0.004s] -Searching alignments... [0.076s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.016s] -Building query seed array... [0.014s] -Computing hash join... [0.005s] -Building seed filter... [0.004s] -Searching alignments... [0.074s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.014s] -Building query seed array... [0.016s] -Computing hash join... [0.006s] -Building seed filter... [0.004s] -Searching alignments... [0.078s] -Deallocating buffers... [0.001s] -Computing alignments... [1.574s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.849s -Reported 351084 pairwise alignments, 351138 HSPs. -29361 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Gl02 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Gl02 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Gl02 - - -There were 31505 ORFs originally, with 925 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 31505 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1258 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4912 Unique ORFs for Sr_rh_Gl02 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca/Original/Concatenated/Sr_rh_Esca.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.018s] -Masking sequences... [0.125s] -Writing sequences... [0.005s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = a6ba9de57b7334a769b88bd0f22acf5b -Processed 11092 sequences, 3356704 letters. -Total time = 0.154s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Esca/Original/Concatenated/Sr_rh_Esca.AA.Concatenated.dmnd -Sequences = 11092 -Letters = 3356704 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.021s] -Masking queries... [0.021s] -Building query seed set... [0.021s] -Algorithm: Double-indexed -Building query histograms... [0.01s] -Allocating buffers... [0s] -Loading reference sequences... [0.012s] -Masking reference... [0.013s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.007s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.014s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... 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[0.003s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.011s] -Building query seed array... [0.011s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.011s] -Building query seed array... [0.009s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.021s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.011s] -Building query seed array... [0.011s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.022s] -Deallocating buffers... [0s] -Computing alignments... [0.27s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 0.867s -Reported 80939 pairwise alignments, 80941 HSPs. -8644 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Esca at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Esca - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Esca - - -There were 11092 ORFs originally, with 697 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 11092 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 491 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 3480 Unique ORFs for Sr_rh_Esca - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03/Original/Concatenated/Sr_rh_Bv03.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.032s] -Masking sequences... [0.028s] -Writing sequences... [0.011s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 7d2fb8d327ed29a308fc6adf9481fe27 -Processed 23147 sequences, 6331934 letters. -Total time = 0.079s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv03/Original/Concatenated/Sr_rh_Bv03.AA.Concatenated.dmnd -Sequences = 23147 -Letters = 6331934 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.033s] -Masking queries... [0.026s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.019s] -Allocating buffers... [0s] -Loading reference sequences... [0.017s] -Masking reference... [0.02s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.012s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.019s] -Building query seed array... [0.018s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.084s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.018s] -Building query seed array... [0.02s] -Computing hash join... [0.003s] -Building seed filter... [0.005s] -Searching alignments... [0.074s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.021s] -Building query seed array... [0.019s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.07s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.018s] -Building query seed array... [0.021s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.067s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.018s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.067s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.021s] -Building query seed array... [0.021s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.059s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.018s] -Building query seed array... [0.018s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.058s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.019s] -Building query seed array... [0.019s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.059s] -Deallocating buffers... [0.001s] -Computing alignments... [0.952s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 2.056s -Reported 269959 pairwise alignments, 269963 HSPs. -19405 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Bv03 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Bv03 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Bv03 - - -There were 23147 ORFs originally, with 1552 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 23147 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1372 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 5015 Unique ORFs for Sr_rh_Bv03 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa/Original/Concatenated/Sr_rh_Sspa.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.026s] -Masking sequences... [0.025s] -Writing sequences... [0.007s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 73ca9ebb7bc1f11c92eff313afe8d09e -Processed 15066 sequences, 4394283 letters. -Total time = 0.064s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Sspa/Original/Concatenated/Sr_rh_Sspa.AA.Concatenated.dmnd -Sequences = 15066 -Letters = 4394283 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.025s] -Masking queries... [0.022s] -Building query seed set... [0.031s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.015s] -Masking reference... [0.017s] -Initializing temporary storage... [0.011s] -Building reference histograms... [0.012s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.017s] -Building query seed array... [0.023s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... 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[0.004s] -Searching alignments... [0.025s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.014s] -Building query seed array... [0.017s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.026s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.018s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.023s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.013s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.005s] -Searching alignments... [0.027s] -Deallocating buffers... [0s] -Computing alignments... [0.306s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 0.987s -Reported 81557 pairwise alignments, 81557 HSPs. -11553 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Sspa at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Sspa - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Sspa - - -There were 15066 ORFs originally, with 934 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 15066 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 955 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 5007 Unique ORFs for Sr_rh_Sspa - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb/Original/Concatenated/Sr_rh_Halb.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.028s] -Masking sequences... [0.027s] -Writing sequences... [0.009s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = be446b493c85f79b57f24c5868ac0c4c -Processed 14869 sequences, 6087712 letters. -Total time = 0.071s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Halb/Original/Concatenated/Sr_rh_Halb.AA.Concatenated.dmnd -Sequences = 14869 -Letters = 6087712 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.029s] -Masking queries... [0.024s] -Building query seed set... [0.027s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.015s] -Masking reference... [0.018s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.013s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.018s] -Building query seed array... [0.017s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... 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[0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.682s -Reported 153389 pairwise alignments, 153474 HSPs. -13522 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Halb at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Halb - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Halb - - -There were 14869 ORFs originally, with 3233 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 14869 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 309 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 2652 Unique ORFs for Sr_rh_Halb - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04/Original/Concatenated/Sr_rh_Bv04.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.033s] -Masking sequences... [0.03s] -Writing sequences... [0.011s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 7d1e6c82caa1170cabd2b9c12a903852 -Processed 21474 sequences, 6727927 letters. -Total time = 0.082s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Bv04/Original/Concatenated/Sr_rh_Bv04.AA.Concatenated.dmnd -Sequences = 21474 -Letters = 6727927 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.04s] -Masking queries... [0.03s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.016s] -Allocating buffers... [0s] -Loading reference sequences... [0.018s] -Masking reference... [0.021s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.014s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.018s] -Building query seed array... [0.018s] -Computing hash join... [0.005s] -Building seed filter... [0.003s] -Searching alignments... 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[0.004s] -Searching alignments... [0.063s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.019s] -Building query seed array... [0.022s] -Computing hash join... [0.005s] -Building seed filter... [0.003s] -Searching alignments... [0.072s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.021s] -Building query seed array... [0.019s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.051s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.015s] -Building query seed array... [0.018s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.055s] -Deallocating buffers... [0s] -Computing alignments... [1.096s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0.001s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.197s -Reported 262985 pairwise alignments, 263041 HSPs. -18915 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Bv04 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Bv04 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Bv04 - - -There were 21474 ORFs originally, with 1156 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 21474 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 848 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4346 Unique ORFs for Sr_rh_Bv04 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01/Original/Concatenated/Sr_rh_Nn01.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.034s] -Masking sequences... [0.031s] -Writing sequences... [0.01s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = d53a7002a89335cfb90dd79e5cf900d7 -Processed 22715 sequences, 6753119 letters. -Total time = 0.083s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn01/Original/Concatenated/Sr_rh_Nn01.AA.Concatenated.dmnd -Sequences = 22715 -Letters = 6753119 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.036s] -Masking queries... [0.029s] -Building query seed set... [0.036s] -Algorithm: Double-indexed -Building query histograms... [0.014s] -Allocating buffers... [0s] -Loading reference sequences... [0.019s] -Masking reference... [0.02s] -Initializing temporary storage... [0.01s] -Building reference histograms... [0.013s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.019s] -Building query seed array... [0.012s] -Computing hash join... [0.005s] -Building seed filter... [0.004s] -Searching alignments... [0.214s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.022s] -Building query seed array... [0.014s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.154s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.018s] -Building query seed array... [0.016s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.173s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.018s] -Building query seed array... [0.012s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.15s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.016s] -Building query seed array... [0.013s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.149s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.018s] -Building query seed array... [0.014s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.123s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.016s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.142s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.014s] -Building query seed array... [0.01s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.132s] -Deallocating buffers... [0.001s] -Computing alignments... [0.996s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 2.749s -Reported 234923 pairwise alignments, 234933 HSPs. -18619 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn01 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn01 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn01 - - -There were 22715 ORFs originally, with 2722 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 22715 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1826 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 5092 Unique ORFs for Sr_rh_Nn01 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01/Original/Concatenated/Sr_rh_Tx01.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.035s] -Masking sequences... [0.03s] -Writing sequences... [0.011s] -Hashing sequences... [0.002s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 5c42afa531e715892722c3aab558955f -Processed 19985 sequences, 6911292 letters. -Total time = 0.084s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Tx01/Original/Concatenated/Sr_rh_Tx01.AA.Concatenated.dmnd -Sequences = 19985 -Letters = 6911292 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.035s] -Masking queries... [0.027s] -Building query seed set... [0.029s] -Algorithm: Double-indexed -Building query histograms... [0.015s] -Allocating buffers... [0s] -Loading reference sequences... [0.019s] -Masking reference... [0.02s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.014s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.018s] -Building query seed array... [0.01s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.123s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.016s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.104s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.016s] -Building query seed array... [0.015s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.099s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.013s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.096s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.014s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.094s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.013s] -Building query seed array... [0.011s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.088s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.014s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.098s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.013s] -Building query seed array... [0.012s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.099s] -Deallocating buffers... [0.001s] -Computing alignments... [0.886s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 2.149s -Reported 249989 pairwise alignments, 250001 HSPs. -18701 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Tx01 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Tx01 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Tx01 - - -There were 19985 ORFs originally, with 5250 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 19985 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 353 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 3027 Unique ORFs for Sr_rh_Tx01 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09/Original/Concatenated/Sr_rh_Nn09.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.043s] -Masking sequences... [0.034s] -Writing sequences... [0.014s] -Hashing sequences... [0.003s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 442d2660d19d6736d72315a56ba66c98 -Processed 30042 sequences, 8360487 letters. -Total time = 0.1s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn09/Original/Concatenated/Sr_rh_Nn09.AA.Concatenated.dmnd -Sequences = 30042 -Letters = 8360487 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.055s] -Masking queries... [0.036s] -Building query seed set... [0.034s] -Algorithm: Double-indexed -Building query histograms... [0.022s] -Allocating buffers... [0s] -Loading reference sequences... [0.023s] -Masking reference... [0.023s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.016s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.023s] -Building query seed array... [0.016s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.342s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.018s] -Building query seed array... [0.012s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.283s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.019s] -Building query seed array... [0.015s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.298s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.02s] -Building query seed array... [0.016s] -Computing hash join... [0.005s] -Building seed filter... [0.003s] -Searching alignments... [0.243s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.019s] -Building query seed array... [0.012s] -Computing hash join... [0.005s] -Building seed filter... [0.004s] -Searching alignments... [0.269s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.023s] -Building query seed array... [0.015s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.225s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.021s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.251s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.022s] -Building query seed array... [0.012s] -Computing hash join... [0.004s] -Building seed filter... [0.004s] -Searching alignments... [0.239s] -Deallocating buffers... [0.001s] -Computing alignments... [1.535s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0.001s] -Deallocating queries... 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[0s] -Total time = 4.28s -Reported 355048 pairwise alignments, 355055 HSPs. -25203 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn09 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn09 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn09 - - -There were 30042 ORFs originally, with 4549 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 30042 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 2368 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 5956 Unique ORFs for Sr_rh_Nn09 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01/Original/Concatenated/Sr_rh_Gl01.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.003s] -Masking sequences... [0.016s] -Writing sequences... [0s] -Hashing sequences... [0s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 527bc5ca7392445b7844cb181d0620f1 -Processed 1224 sequences, 170624 letters. -Total time = 0.023s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Gl01/Original/Concatenated/Sr_rh_Gl01.AA.Concatenated.dmnd -Sequences = 1224 -Letters = 170624 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.001s] -Masking queries... [0.014s] -Building query seed set... [0.004s] -Algorithm: Double-indexed -Building query histograms... [0.002s] -Allocating buffers... [0s] -Loading reference sequences... [0.001s] -Masking reference... [0.007s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.003s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.013s] -Building query seed array... [0.014s] -Computing hash join... [0.002s] -Building seed filter... [0.007s] -Searching alignments... 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[0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.011s] -Building query seed array... [0.008s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.007s] -Building query seed array... [0.006s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.009s] -Building query seed array... [0.006s] -Computing hash join... [0.002s] -Building seed filter... [0.003s] -Searching alignments... [0.004s] -Deallocating buffers... [0s] -Computing alignments... [0.036s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... 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[0s] -Total time = 0.331s -Reported 4157 pairwise alignments, 4157 HSPs. -594 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Gl01 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Gl01 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Gl01 - - -There were 1224 ORFs originally, with 32 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 1224 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 44 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 667 Unique ORFs for Sr_rh_Gl01 - - -Next Script is: 6b_update_cov_post_removepartials.py - - -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 64 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Database file: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14/Original/Concatenated/Sr_rh_Nn14.AA.Concatenated.fasta -Opening the database file... [0.002s] -Loading sequences... [0.028s] -Masking sequences... [0.027s] -Writing sequences... [0.01s] -Hashing sequences... [0.001s] -Loading sequences... [0s] -Writing trailer... [0s] -Closing the input file... [0s] -Closing the database file... [0s] -Database hash = 2cefd71c2b2dfc7c97c47bb5141899b8 -Processed 17441 sequences, 5176642 letters. -Total time = 0.071s -diamond v0.9.30.131 (C) Max Planck Society for the Advancement of Science -Documentation, support and updates available at http://www.diamondsearch.org - -#CPU threads: 60 -Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14/Original/Concatenated/SpreadSheets -Opening the database... [0.001s] -#Target sequences to report alignments for: 25 -Reference = /beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams//Output/Sr_rh_Nn14/Original/Concatenated/Sr_rh_Nn14.AA.Concatenated.dmnd -Sequences = 17441 -Letters = 5176642 -Block size = 2000000000 -Opening the input file... [0s] -Opening the output file... [0s] -Loading query sequences... [0.027s] -Masking queries... [0.025s] -Building query seed set... [0.033s] -Algorithm: Double-indexed -Building query histograms... [0.012s] -Allocating buffers... [0s] -Loading reference sequences... [0.014s] -Masking reference... [0.017s] -Initializing temporary storage... [0.009s] -Building reference histograms... [0.015s] -Allocating buffers... [0s] -Processing query block 0, reference block 0, shape 0, index chunk 0. -Building reference seed array... [0.021s] -Building query seed array... [0.017s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.055s] -Processing query block 0, reference block 0, shape 0, index chunk 1. -Building reference seed array... [0.014s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 0, index chunk 2. -Building reference seed array... [0.015s] -Building query seed array... [0.015s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.052s] -Processing query block 0, reference block 0, shape 0, index chunk 3. -Building reference seed array... [0.019s] -Building query seed array... [0.017s] -Computing hash join... [0.004s] -Building seed filter... [0.003s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 1, index chunk 0. -Building reference seed array... [0.014s] -Building query seed array... [0.02s] -Computing hash join... [0.004s] -Building seed filter... [0.005s] -Searching alignments... [0.042s] -Processing query block 0, reference block 0, shape 1, index chunk 1. -Building reference seed array... [0.016s] -Building query seed array... [0.017s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.038s] -Processing query block 0, reference block 0, shape 1, index chunk 2. -Building reference seed array... [0.016s] -Building query seed array... [0.018s] -Computing hash join... [0.003s] -Building seed filter... [0.004s] -Searching alignments... [0.04s] -Processing query block 0, reference block 0, shape 1, index chunk 3. -Building reference seed array... [0.017s] -Building query seed array... [0.016s] -Computing hash join... [0.003s] -Building seed filter... [0.003s] -Searching alignments... [0.041s] -Deallocating buffers... [0s] -Computing alignments... [0.496s] -Deallocating reference... [0s] -Loading reference sequences... [0s] -Deallocating buffers... [0s] -Deallocating queries... [0s] -Loading query sequences... [0s] -Closing the input file... [0s] -Closing the output file... [0s] -Closing the database file... [0s] -Deallocating taxonomy... [0s] -Total time = 1.358s -Reported 124839 pairwise alignments, 124844 HSPs. -13517 queries aligned. - - -Merging Transcriptome data together. - - -Binning ALL Nucleotide ORFs for Sr_rh_Nn14 at 98% identity. - - - - -Removing Partial ORFs with >98% Nucleotide Identity over >70% of -their length when compared to more complete ORFs from: Sr_rh_Nn14 - - -Removing Abnormally Short (70% length) OR Long (200% length) ORFs -compared to typical Gene Family member length for: Sr_rh_Nn14 - - -There were 17441 ORFs originally, with 663 Partial ORFs that -were 100% Identical to larger ORFs. - - -Of the 17441 original ORFs, 0 are Partial ORFs (e.g. > 98% -NUCLEOTIDE identity) to larger ORFs with 1588 additional ORFs -that were either TOO LONG or SHORT. - - -Overall, there are 4906 Unique ORFs for Sr_rh_Nn14 - - -Next Script is: 6b_update_cov_post_removepartials.py - - - - -Renaming Sr_rh_Esca's files with the following 10-character -code: Sr_rh_Esca - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Esca_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Esca files can be -found in the Sr_rh_Esca and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn05's files with the following 10-character -code: Sr_rh_Nn05 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn05_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn05 files can be -found in the Sr_rh_Nn05 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Bv04's files with the following 10-character -code: Sr_rh_Bv04 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Bv04_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Bv04 files can be -found in the Sr_rh_Bv04 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn10's files with the following 10-character -code: Sr_rh_Nn10 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn10_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn10 files can be -found in the Sr_rh_Nn10 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Bv03's files with the following 10-character -code: Sr_rh_Bv03 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Bv03_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Bv03 files can be -found in the Sr_rh_Bv03 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn14's files with the following 10-character -code: Sr_rh_Nn14 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn14_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn14 files can be -found in the Sr_rh_Nn14 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn03's files with the following 10-character -code: Sr_rh_Nn03 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn03_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn03 files can be -found in the Sr_rh_Nn03 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Bv02's files with the following 10-character -code: Sr_rh_Bv02 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Bv02_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Bv02 files can be -found in the Sr_rh_Bv02 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn07's files with the following 10-character -code: Sr_rh_Nn07 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn07_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn07 files can be -found in the Sr_rh_Nn07 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Hhir's files with the following 10-character -code: Sr_rh_Hhir - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Hhir_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Hhir files can be -found in the Sr_rh_Hhir and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Gl01's files with the following 10-character -code: Sr_rh_Gl01 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Gl01_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Gl01 files can be -found in the Sr_rh_Gl01 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Gsp1's files with the following 10-character -code: Sr_rh_Gsp1 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Gsp1_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Gsp1 files can be -found in the Sr_rh_Gsp1 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Rsp1's files with the following 10-character -code: Sr_rh_Rsp1 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Rsp1_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Rsp1 files can be -found in the Sr_rh_Rsp1 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Calb's files with the following 10-character -code: Sr_rh_Calb - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Calb_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Calb files can be -found in the Sr_rh_Calb and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn09's files with the following 10-character -code: Sr_rh_Nn09 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn09_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn09 files can be -found in the Sr_rh_Nn09 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn08's files with the following 10-character -code: Sr_rh_Nn08 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn08_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn08 files can be -found in the Sr_rh_Nn08 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn01's files with the following 10-character -code: Sr_rh_Nn01 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn01_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn01 files can be -found in the Sr_rh_Nn01 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Bv06's files with the following 10-character -code: Sr_rh_Bv06 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Bv06_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Bv06 files can be -found in the Sr_rh_Bv06 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn02's files with the following 10-character -code: Sr_rh_Nn02 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn02_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn02 files can be -found in the Sr_rh_Nn02 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Bv05's files with the following 10-character -code: Sr_rh_Bv05 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Bv05_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Bv05 files can be -found in the Sr_rh_Bv05 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Sspa's files with the following 10-character -code: Sr_rh_Sspa - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Sspa_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Sspa files can be -found in the Sr_rh_Sspa and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Hind's files with the following 10-character -code: Sr_rh_Hind - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Hind_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Hind files can be -found in the Sr_rh_Hind and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn12's files with the following 10-character -code: Sr_rh_Nn12 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn12_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn12 files can be -found in the Sr_rh_Nn12 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Gspa's files with the following 10-character -code: Sr_rh_Gspa - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Gspa_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Gspa files can be -found in the Sr_rh_Gspa and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Bv01's files with the following 10-character -code: Sr_rh_Bv01 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Bv01_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Bv01 files can be -found in the Sr_rh_Bv01 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Tx01's files with the following 10-character -code: Sr_rh_Tx01 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Tx01_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Tx01 files can be -found in the Sr_rh_Tx01 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn06's files with the following 10-character -code: Sr_rh_Nn06 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn06_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn06 files can be -found in the Sr_rh_Nn06 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn04's files with the following 10-character -code: Sr_rh_Nn04 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn04_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn04 files can be -found in the Sr_rh_Nn04 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Gl02's files with the following 10-character -code: Sr_rh_Gl02 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Gl02_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Gl02 files can be -found in the Sr_rh_Gl02 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Slin's files with the following 10-character -code: Sr_rh_Slin - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Slin_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Slin files can be -found in the Sr_rh_Slin and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Emar's files with the following 10-character -code: Sr_rh_Emar - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Emar_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Emar files can be -found in the Sr_rh_Emar and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn13's files with the following 10-character -code: Sr_rh_Nn13 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn13_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn13 files can be -found in the Sr_rh_Nn13 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Emac's files with the following 10-character -code: Sr_rh_Emac - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Emac_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Emac files can be -found in the Sr_rh_Emac and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Halb's files with the following 10-character -code: Sr_rh_Halb - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Halb_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Halb files can be -found in the Sr_rh_Halb and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Atps's files with the following 10-character -code: Sr_rh_Atps - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Atps_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Atps files can be -found in the Sr_rh_Atps and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Nn11's files with the following 10-character -code: Sr_rh_Nn11 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Nn11_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Nn11 files can be -found in the Sr_rh_Nn11 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Gl03's files with the following 10-character -code: Sr_rh_Gl03 - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Gl03_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Gl03 files can be -found in the Sr_rh_Gl03 and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - - - -Renaming Sr_rh_Usac's files with the following 10-character -code: Sr_rh_Usac - - -Renaming Translated (Protein) ORFs - - -Renaming Nucleotide ORFs - - -Updating CDS Names in the Spreadsheet - - -Converting Sr_rh_Usac_Filtered.UC.Final.AA.ORF.fasta to XML format - - -There is no next script! The final Sr_rh_Usac files can be -found in the Sr_rh_Usac and ReadyToGo folders and are ready -for the KatzLab Phylogenomic Tree-Building Steps! - - -Traceback (most recent call last): - File "8_SummaryStats.py", line 8, in - import matplotlib.pyplot as plt -ModuleNotFoundError: No module named 'matplotlib' - -Running script 1... - - -Running script 2... - - -Running script 3... - - -Running script 4... - - -Running script 5... - - -Running script 6... - - -Running script 7... -