#t2ac: EvidentialGene tr2aacds.pl VERSION 2013.07.27 #t2ac: app=blastn, path=/home/ux455375/bio/ncbi2227/bin/blastn #t2ac: app=makeblastdb, path=/home/ux455375/bio/ncbi2227/bin/makeblastdb #t2ac: app=lastz, path=/home/ux455375/bio/bin/lastz #t2ac: app=fastanrdb, path=/home/ux455375/bio/exonerate/bin/fastanrdb #t2ac: app=cd-hit-est, path=/home/ux455375/bio/cdhit/bin/cd-hit-est #t2ac: app=cd-hit, path=/home/ux455375/bio/cdhit/bin/cd-hit #t2ac: evigeneapp=cdna_bestorf.pl, path=/home/ux455375/bio/evigene/scripts/prot/../cdna_bestorf.pl #t2ac: evigeneapp=prot/traa2cds.pl, path=/home/ux455375/bio/evigene/scripts/prot/../prot/traa2cds.pl #t2ac: evigeneapp=rnaseq/asmrna_dupfilter2.pl, path=/home/ux455375/bio/evigene/scripts/prot/../rnaseq/asmrna_dupfilter2.pl #t2ac: evigeneapp=prot/aaqual.sh, path=/home/ux455375/bio/evigene/scripts/prot/../prot/aaqual.sh #t2ac: BEGIN with cdnaseq= evg3hbee.tr date= Thu May 1 14:16:23 PDT 2014 #t2ac: bestorf_cds= evg3hbee.cds nrec= 6156631 #t2ac: nonredundant_cds= evg3hbeenr.cds nrec= 2257631 #t2ac: CMD= touch evg3hbeenr.cds.isbest #t2ac: nonredundant_reassignbest= 0 of 761750 #t2ac: CMD= /home/ux455375/bio/cdhit/bin/cd-hit-est -c 1.00 -T 24 -M 60000 -l 89 -d 0 -i evg3hbeenr.cds -o evg3hbeenrcd1.cds 1> evg3hbeenrcd1.log 2>&1 #t2ac: nofragments_cds= evg3hbeenrcd1.cds nrec= 1353185 #t2ac: CMD= /home/ux455375/bio/ncbi2227/bin/makeblastdb -in evg3hbeenrcd1.cds -dbtype nucl -out evg3hbeenrcd1_db -logfile evg3hbeenrcd1_db.log #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split1.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split1-self98.blastn1 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split2.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split2-self98.blastn2 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split3.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split3-self98.blastn3 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split4.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split4-self98.blastn4 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split5.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split5-self98.blastn5 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split6.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split6-self98.blastn6 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split7.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split7-self98.blastn7 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split8.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split8-self98.blastn8 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split9.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split9-self98.blastn9 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split10.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split10-self98.blastn10 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split11.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split11-self98.blastn11 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split12.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split12-self98.blastn12 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split13.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split13-self98.blastn13 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split14.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split14-self98.blastn14 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split15.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split15-self98.blastn15 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split16.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split16-self98.blastn16 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split17.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split17-self98.blastn17 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split18.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split18-self98.blastn18 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split19.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split19-self98.blastn19 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split20.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split20-self98.blastn20 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split21.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split21-self98.blastn21 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split22.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split22-self98.blastn22 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split23.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split23-self98.blastn23 #t2ac: forkCMD= /home/ux455375/bio/ncbi2227/bin/blastn -task megablast -perc_identity 98 -evalue 1e-19 -ungapped -dust no -outfmt 7 -db evg3hbeenrcd1_db -query evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split24.fa -out evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split24-self98.blastn24 #t2ac: CMD= cat evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split1-self98.blastn1 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split2-self98.blastn2 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split3-self98.blastn3 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split4-self98.blastn4 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split5-self98.blastn5 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split6-self98.blastn6 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split7-self98.blastn7 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split8-self98.blastn8 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split9-self98.blastn9 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split10-self98.blastn10 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split11-self98.blastn11 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split12-self98.blastn12 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split13-self98.blastn13 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split14-self98.blastn14 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split15-self98.blastn15 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split16-self98.blastn16 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split17-self98.blastn17 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split18-self98.blastn18 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split19-self98.blastn19 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split20-self98.blastn20 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split21-self98.blastn21 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split22-self98.blastn22 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split23-self98.blastn23 evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split24-self98.blastn24 > evg3hbeenrcd1-self98.blastn #t2ac: blastn_cds= evg3hbeenrcd1-self98.blastn #t2ac: CMD= /home/ux455375/bio/cdhit/bin/cd-hit -T 24 -M 60000 -l 30 -c 0.90 -d 0 -i evg3hbee.aa -o evg3hbee_cd90.aa 1> evg3hbee_cd90.log 2>&1 #t2ac: CMD= /home/ux455375/bio/evigene/scripts/prot/../rnaseq/asmrna_dupfilter2.pl -debug -tinyaln 35 -aasize evg3hbee.aa.qual -CDSALIGN -blastab evg3hbeenrcd1-self98.blastn -acdhit evg3hbee_cd90.aa.clstr -outeqtab evg3hbee.alntab -outclass evg3hbee.trclass >evg3hbee.adupfilt.log 2>&1 #t2ac: asmdupfilter_cds= evg3hbee.trclass # Class Table for evg3hbee.trclass class okay drop okay drop althi 4.5 11.4 61969 154724 althi1 8.8 24.4 119671 331456 althia2 0 0.5 0 7687 altmfrag 0.4 0.4 6271 6534 altmfraga2 0 0 696 631 altmid 0.6 0.6 8381 9294 altmida2 0 0 690 498 main 4.4 4.6 60370 62381 maina2 0.3 0.2 4868 3490 noclass 2.3 7.7 32321 105044 noclassa2 0 0 138 166 parthi 0 16.2 0 220332 parthi1 0 9 0 122333 parthia2 0 2.4 0 33187 --------------------------------------------- total 21.8 78.1 295375 1057757 ============================================= # AA-quality for okay set of evg3hbee.aa.qual (no okalt): all and longest 1000 summary okay.top n=1000; average=2024; median=1725; min,max=1362,16948; sum=2024541; gaps=9430,9.4 okay.all n=97697; average=217; median=131; min,max=40,16948; sum=21253925; gaps=681261,6.9 #t2ac: asmdupfilter_fileset= evg3hbee.okay.tr evg3hbee.okalt.tr evg3hbee.drop.tr evg3hbee.okay.aa evg3hbee.okalt.aa evg3hbee.drop.aa evg3hbee.okay.cds evg3hbee.okalt.cds evg3hbee.drop.cds #t2ac: tidyup output folders: okayset dropset inputset tmpfiles #t2ac: CMD= mv evg3hbee.okay.tr okayset/evg3hbee.okay.tr #t2ac: CMD= mv evg3hbee.okalt.tr okayset/evg3hbee.okalt.tr #t2ac: CMD= mv evg3hbee.okay.aa okayset/evg3hbee.okay.aa #t2ac: CMD= mv evg3hbee.okalt.aa okayset/evg3hbee.okalt.aa #t2ac: CMD= mv evg3hbee.okay.cds okayset/evg3hbee.okay.cds #t2ac: CMD= mv evg3hbee.okalt.cds okayset/evg3hbee.okalt.cds #t2ac: CMD= mv evg3hbee.drop.tr dropset/evg3hbee.drop.tr #t2ac: CMD= mv evg3hbee.drop.aa dropset/evg3hbee.drop.aa #t2ac: CMD= mv evg3hbee.drop.cds dropset/evg3hbee.drop.cds #t2ac: CMD= mv evg3hbee.cds inputset/evg3hbee.cds #t2ac: CMD= mv evg3hbee.aa inputset/evg3hbee.aa #t2ac: CMD= mv evg3hbee.aa.qual inputset/evg3hbee.aa.qual #t2ac: CMD= mv evg3hbeenr.cds tmpfiles/evg3hbeenr.cds #t2ac: CMD= mv evg3hbeenr.cds.isbest tmpfiles/evg3hbeenr.cds.isbest #t2ac: CMD= mv evg3hbeenrcd1.cds tmpfiles/evg3hbeenrcd1.cds #t2ac: CMD= mv evg3hbeenrcd1.cds.clstr tmpfiles/evg3hbeenrcd1.cds.clstr #t2ac: CMD= mv evg3hbeenrcd1.log tmpfiles/evg3hbeenrcd1.log #t2ac: CMD= mv evg3hbeenrcd1-self98.blastn tmpfiles/evg3hbeenrcd1-self98.blastn #t2ac: CMD= mv evg3hbeenrcd1_db.log tmpfiles/evg3hbeenrcd1_db.log #t2ac: CMD= mv evg3hbee_cd90.aa tmpfiles/evg3hbee_cd90.aa #t2ac: CMD= mv evg3hbee_cd90.aa.clstr tmpfiles/evg3hbee_cd90.aa.clstr #t2ac: CMD= mv evg3hbee_cd90.log tmpfiles/evg3hbee_cd90.log #t2ac: CMD= mv evg3hbee.alntab tmpfiles/evg3hbee.alntab #t2ac: CMD= mv evg3hbee.adupfilt.log tmpfiles/evg3hbee.adupfilt.log #t2ac: tidyup erase: n=51, evg3hbeenrcd1_db.nsq evg3hbeenrcd1_db.nin evg3hbeenrcd1_db.nhr evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split1.fa evg3hbeenrcd1_blsplit/evg3hbeenrcd1.split2.fa .. #t2ac: DONE at date= Thu May 1 19:05:45 PDT 2014 #t2ac: ======================================