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EukPhylo/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/log
Katzlab dd76ab1d12 Added PTL2 Scripts 
These are PTL2 files from Auden 2/9
2023-02-14 11:20:52 -05:00

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========================================= NEW GUIDANCE RUN STARTED ===========================================
GUIDANCE COMMAND: perl guidance.v2.02/www/Guidance/guidance.pl --bootstraps 10 --seqFile batch2/OG5_126554_0_preguidance.fasta --msaProgram MAFFT --seqType aa --outDir /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance --seqCutoff 0.7 --colCutoff 0.4 --outOrder as_input --MSA_Param \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol
Guidance::validate_Seqs(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/,Seqs.Orig.fas,AminoAcids,No): return: OK Seqs.Orig.fas.FIXED 64
Guidance::name2codeFastaFrom1(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED, /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes, /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas,0,seqNum);
convert_fs_to_upper_case(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas)
Align: mafft \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --amino --quiet /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas > /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln
Bootstrap_Trees: /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/../../programs/semphy/semphy -a 20 --jtt -H -J -v 8 --BPrepeats=10 -s /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln -o /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.out -T /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.outTree -l /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.log > /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.std
Guidance::pullOutBPtrees(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/,MSA,10,MAFFT);
Guidance::root_BP_trees(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/,MSA, MAFFT, 10,"",BioPerl);
Sample op according to uniform distribution: Guidance::SampleFromUnifomDist(1,3,/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//SampledOPVals.log,10)
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_0 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_0/MSA.MAFFT.semphy.tree_0.rooted.GoodBranchLength 19 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.000817428956 >> COS.std
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_1 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_1/MSA.MAFFT.semphy.tree_1.rooted.GoodBranchLength 108 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.58462865668747 >> COS.std
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_2 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_2/MSA.MAFFT.semphy.tree_2.rooted.GoodBranchLength 82 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 1.49936059497511 >> COS.std
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_3 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_3/MSA.MAFFT.semphy.tree_3.rooted.GoodBranchLength 60 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 1.23331485380722 >> COS.std
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_4 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_4/MSA.MAFFT.semphy.tree_4.rooted.GoodBranchLength 76 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.15783221114012 >> COS.std
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_5 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_5/MSA.MAFFT.semphy.tree_5.rooted.GoodBranchLength 53 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.90590667209469 >> COS.std
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_6 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_6/MSA.MAFFT.semphy.tree_6.rooted.GoodBranchLength 57 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.63676633992571 >> COS.std
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_7 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_7/MSA.MAFFT.semphy.tree_7.rooted.GoodBranchLength 100 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.80645936921989 >> COS.std
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_8 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_8/MSA.MAFFT.semphy.tree_8.rooted.GoodBranchLength 72 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 1.84405518368005 >> COS.std
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_9 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_9/MSA.MAFFT.semphy.tree_9.rooted.GoodBranchLength 24 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.13819830457351 >> COS.std
calculating SP scores: /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/../../programs/msa_set_score/msa_set_score /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.aln /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.Guidance2 -d /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/GUIDANCE2_MSA/ > /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.msa_set_score.std
Guidance::codes2name_scoresFile_NEW("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names");
Guidance::removeLowSPsites_NoBioPerl ("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Without_low_SP_Col",0.4,"/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.MSA.MAFFT.Removed_Col");
REMOVED_SITES:0
MSA_LENGTH:351
ans=Convert_to_CSV("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv");
ANS:OK
Guidance::printColoredAlignment_With_CSS("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance_res_pair_res.html","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_res.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv",GUIDANCE2,"/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr");
1Guidance::removeLowSPseq ("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Without_low_SP_Seq",0.7,"/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Removed_Seq");
Guidance::make_Jalview_Color_MSA("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_res.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_JalView_Features","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes");
Guidance::make_Jalview_AnnotationGraph("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_JalView_Annot","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv",GUIDANCE2." scores");
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