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... [0.08s] Processing query block 0, reference block 0, shape 0, 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... [0.064s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.021s] 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 0, index chunk 3. Building reference seed array... [0.016s] Building query seed array... [0.013s] Computing hash join... [0.004s] Building seed filter... [0.004s] Searching alignments... [0.058s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.01s] 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 1. Building reference seed array... [0.014s] Building query seed array... [0.013s] Computing hash join... [0.004s] Building seed filter... [0.004s] Searching alignments... [0.063s] Processing query block 0, reference block 0, shape 1, index chunk 2. Building reference seed array... [0.014s] Building query seed array... [0.013s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.077s] Processing query block 0, reference block 0, shape 1, index chunk 3. Building reference seed array... [0.016s] Building query seed array... [0.009s] Computing hash join... [0.004s] Building seed filter... [0.003s] Searching alignments... [0.053s] Deallocating buffers... [0s] Computing alignments... [1.01s] 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 = 2.041s 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... [0.035s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.014s] Building query seed array... [0.015s] Computing hash join... [0.003s] 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... [0.012s] Building query seed array... [0.018s] Computing hash join... [0.003s] 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... [0.011s] Building query seed array... [0.015s] Computing hash join... [0.004s] Building seed filter... [0.004s] Searching alignments... [0.029s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.012s] Building query seed array... [0.012s] Computing hash join... [0.004s] Building seed filter... [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... [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 = 1.045s 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... [0.075s] Processing query block 0, reference block 0, shape 0, 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... [0.06s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.011s] Building query seed array... [0.014s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.054s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.01s] Building query seed array... [0.01s] Computing hash join... [0.003s] 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... [0.011s] Building query seed array... [0.01s] Computing hash join... [0.003s] 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... [0.012s] 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... [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 = 1.57s 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... [0.054s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.016s] Building query seed array... [0.018s] Computing hash join... [0.003s] 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... [0.016s] Building query seed array... [0.019s] Computing hash join... [0.003s] 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... [0.016s] Building query seed array... [0.015s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.055s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.021s] Building query seed array... [0.019s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.046s] 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... [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 = 1.461s 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... [0.047s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.017s] Building query seed array... [0.018s] Computing hash join... [0.003s] 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... [0.018s] Building query seed array... [0.019s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.039s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.014s] Building query seed array... [0.017s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.039s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.016s] Building query seed array... [0.019s] Computing hash join... [0.004s] 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... [0.016s] Building query seed array... [0.015s] Computing hash join... [0.003s] 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... [0.016s] Building query seed array... [0.019s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.034s] 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... [0.003s] Searching alignments... [0.033s] Deallocating buffers... [0s] Computing alignments... [0.486s] 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 = 1.293s 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... [0.032s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.011s] Building query seed array... [0.011s] Computing hash join... [0.002s] 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... [0.013s] 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 0, index chunk 3. Building reference seed array... [0.011s] Building query seed array... [0.007s] 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 0. Building reference seed array... [0.011s] Building query seed array... [0.011s] Computing hash join... [0.004s] Building seed filter... [0.006s] Searching alignments... [0.031s] 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... [0.005s] Building seed filter... [0.007s] Searching alignments... [0.022s] Processing query block 0, reference block 0, shape 1, index chunk 2. Building reference seed array... [0.011s] Building query seed array... [0.013s] 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 3. Building reference seed array... [0.011s] Building query seed array... [0.015s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.023s] Deallocating buffers... [0s] Computing alignments... [0.293s] 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 = 0.903s 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... [0.214s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.019s] Building query seed array... [0.017s] Computing hash join... [0.004s] Building seed filter... [0.005s] Searching alignments... [0.153s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.018s] Building query seed array... [0.015s] Computing hash join... [0.004s] Building seed filter... [0.003s] Searching alignments... [0.147s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.016s] Building query seed array... [0.015s] Computing hash join... [0.004s] Building seed filter... [0.004s] Searching alignments... [0.135s] 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... [0.003s] 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... [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 = 2.825s 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... [0.092s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.013s] Building query seed array... [0.013s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.071s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.012s] Building query seed array... [0.012s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.072s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.011s] Building query seed array... [0.009s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.068s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.014s] Building query seed array... [0.011s] Computing hash join... [0.004s] Building seed filter... [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... [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 = 1.702s 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... [0.048s] Processing query block 0, reference block 0, shape 0, 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... [0.045s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.015s] Building query seed array... [0.017s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.046s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.013s] Building query seed array... [0.017s] 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 0. Building reference seed array... [0.013s] Building query seed array... [0.015s] 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 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... [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 = 1.221s 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... [0.483s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.022s] Building query seed array... [0.016s] Computing hash join... [0.004s] Building seed filter... [0.004s] Searching alignments... [0.347s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.025s] Building query seed array... [0.013s] Computing hash join... [0.004s] Building seed filter... [0.004s] Searching alignments... [0.375s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.021s] Building query seed array... [0.013s] Computing hash join... [0.005s] Building seed filter... [0.004s] Searching alignments... [0.345s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.02s] Building query seed array... [0.011s] Computing hash join... [0.005s] Building seed filter... [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... [0.063s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.019s] Building query seed array... [0.018s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.05s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.015s] Building query seed array... [0.017s] Computing hash join... [0.004s] 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... [0.014s] Building query seed array... [0.016s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.046s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.013s] Building query seed array... [0.015s] 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 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... [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 = 1.582s 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... [0.084s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.019s] Building query seed array... [0.02s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.064s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.022s] Building query seed array... [0.025s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.065s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.016s] Building query seed array... [0.013s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.056s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.016s] Building query seed array... [0.017s] Computing hash join... [0.004s] Building seed filter... [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... [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 = 1.605s 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... [0.1s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.021s] Building query seed array... [0.014s] Computing hash join... [0.005s] Building seed filter... [0.003s] Searching alignments... [0.09s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.021s] Building query seed array... [0.015s] Computing hash join... [0.005s] Building seed filter... [0.003s] Searching alignments... [0.082s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.015s] Building query seed array... [0.017s] Computing hash join... [0.005s] Building seed filter... [0.004s] Searching alignments... [0.082s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.015s] Building query seed array... [0.015s] 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 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... [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 = 2.681s 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... [0.03s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.011s] Building query seed array... [0.006s] Computing hash join... [0.003s] 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... [0.012s] Building query seed array... [0.014s] Computing hash join... [0.003s] 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... [0.011s] Building query seed array... [0.012s] Computing hash join... [0.004s] Building seed filter... [0.004s] Searching alignments... [0.023s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.011s] Building query seed array... [0.014s] Computing hash join... [0.003s] 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... [0.011s] 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 2. Building reference seed array... [0.015s] 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 1, index chunk 3. Building reference seed array... [0.01s] Building query seed array... [0.014s] Computing hash join... [0.003s] Building seed filter... [0.005s] Searching alignments... [0.024s] Deallocating buffers... [0s] Computing alignments... [0.248s] 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 = 0.847s 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... [0.183s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.026s] Building query seed array... [0.017s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.121s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.025s] Building query seed array... [0.02s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.125s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.026s] Building query seed array... [0.014s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.112s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.021s] Building query seed array... [0.014s] Computing hash join... [0.003s] Building seed filter... [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... [0.095s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.02s] Building query seed array... [0.024s] Computing hash join... [0.004s] Building seed filter... [0.007s] Searching alignments... [0.079s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.024s] Building query seed array... [0.023s] Computing hash join... [0.005s] Building seed filter... [0.007s] Searching alignments... [0.071s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.014s] Building query seed array... [0.017s] Computing hash join... [0.004s] Building seed filter... [0.003s] Searching alignments... [0.076s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.018s] Building query seed array... [0.017s] Computing hash join... [0.003s] Building seed filter... [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... [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 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... [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 = 2.059s 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... [0.088s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.024s] Building query seed array... [0.027s] Computing hash join... [0.003s] 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... [0.021s] Building query seed array... [0.02s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.071s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.019s] Building query seed array... [0.026s] Computing hash join... [0.004s] Building seed filter... [0.003s] Searching alignments... [0.068s] 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... [0.004s] Building seed filter... [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... [0.108s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.019s] Building query seed array... [0.017s] Computing hash join... [0.005s] Building seed filter... [0.004s] Searching alignments... [0.084s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.018s] Building query seed array... [0.017s] Computing hash join... [0.006s] Building seed filter... [0.004s] Searching alignments... [0.08s] Processing query block 0, reference block 0, shape 0, 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... [0.089s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.017s] Building query seed array... [0.012s] Computing hash join... [0.005s] Building seed filter... [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... [0.036s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.012s] Building query seed array... [0.015s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.026s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.013s] Building query seed array... [0.014s] Computing hash join... [0.003s] 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... [0.01s] Building query seed array... [0.013s] Computing hash join... [0.002s] Building seed filter... [0.004s] Searching alignments... [0.032s] 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... [0.002s] 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... [0.011s] 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... [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 = 2.056s 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... [0.032s] 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... [0.003s] Searching alignments... [0.028s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.014s] Building query seed array... [0.015s] 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 3. Building reference seed array... [0.011s] Building query seed array... [0.012s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.024s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.011s] Building query seed array... [0.013s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.025s] 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... [0.086s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.018s] Building query seed array... [0.015s] Computing hash join... [0.004s] Building seed filter... [0.004s] Searching alignments... [0.075s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.017s] Building query seed array... [0.018s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.062s] 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... [0.004s] Searching alignments... [0.065s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.022s] Building query seed array... [0.012s] 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 1. Building reference seed array... [0.014s] Building query seed array... [0.014s] 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... [0.02s] Building query seed array... [0.016s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.062s] Processing query block 0, reference block 0, shape 1, index chunk 3. Building reference seed array... [0.014s] Building query seed array... [0.017s] Computing hash join... [0.003s] Building seed filter... [0.004s] Searching alignments... [0.056s] Deallocating buffers... [0s] Computing alignments... [0.649s] 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 = 1.682s 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... [0.081s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.027s] Building query seed array... [0.02s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.07s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.02s] Building query seed array... [0.021s] Computing hash join... [0.003s] Building seed filter... [0.003s] Searching alignments... [0.068s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.017s] Building query seed array... [0.019s] Computing hash join... [0.004s] 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... [0.014s] Building query seed array... [0.018s] Computing hash join... [0.004s] 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... [0.019s] 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... [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 = 2.749s 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... [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 = 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... [0.007s] Processing query block 0, reference block 0, shape 0, index chunk 1. Building reference seed array... [0.008s] Building query seed array... [0.004s] Computing hash join... [0.002s] Building seed filter... [0.004s] Searching alignments... [0.005s] Processing query block 0, reference block 0, shape 0, index chunk 2. Building reference seed array... [0.015s] Building query seed array... [0.007s] Computing hash join... [0.003s] Building seed filter... [0.005s] Searching alignments... [0.005s] Processing query block 0, reference block 0, shape 0, index chunk 3. Building reference seed array... [0.009s] Building query seed array... [0.009s] Computing hash join... [0.002s] Building seed filter... [0.003s] Searching alignments... [0.005s] Processing query block 0, reference block 0, shape 1, index chunk 0. Building reference seed array... [0.011s] Building query seed array... [0.005s] 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 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... [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 = 0.331s 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...