d42b1cf12daaba8db0c8faa736548d6d1edb0f30 hiram Fri Feb 5 13:21:16 2021 -0800 adding make doc for the runs that were all automatic refs #26815 diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt index 0666856..9cdb6db 100644 --- src/hg/makeDb/doc/mm39/lastzRuns.txt +++ src/hg/makeDb/doc/mm39/lastzRuns.txt @@ -1,267 +1,1858 @@ ############################################################################## # LASTZ Great Dane canFam5 (DONE - 2020-08-17 - Hiram) # establish a screen to control this job mkdir /hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17 cd /hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17 printf '# German shepard canFam5 vs mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz BLASTZ_M=254 # TARGET: Mouse Mm39 SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: German shepard canFam5 SEQ2_DIR=/hive/data/genomes/canFam5/canFam5.2bit SEQ2_LEN=/hive/data/genomes/canFam5/chrom.sizes SEQ2_CHUNK=10000000 SEQ2_LIMIT=20 SEQ2_LAP=0 BASE=/hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 & # real 200m16.271s cat fb.mm39.chainCanFam5Link.txt # 778327929 bases of 2654624157 (29.320%) in intersection cat fb.mm39.chainSynCanFam5Link.txt # 735515331 bases of 2654624157 (27.707%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev mm39 canFam5 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 213m30.572s cat fb.mm39.chainRBest.CanFam5.txt # 740738480 bases of 2654624157 (27.904%) in intersection mkdir /hive/data/genomes/canFam5/bed/blastz.mm39.swap cd /hive/data/genomes/canFam5/bed/blastz.mm39.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm39/bed/lastzCanFam5.2020-08-17/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 & # real 44m12.732s cat fb.canFam5.chainMm39Link.txt # 762233776 bases of 2337131234 (32.614%) in intersection cat fb.canFam5.chainSynMm39Link.txt # 731337903 bases of 2337131234 (31.292%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev canFam5 mm39 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 174m14.398s cat fb.canFam5.chainRBest.Mm39.txt # 739648625 bases of 2337131234 (31.648%) in intersection ############################################################################## # LASTZ mouse mm39 vs marmoset calJac4 (DONE - 2020-09-04 - Hiram) # establish a screen to control this job mkdir /hive/data/genomes/mm39/bed/lastzCalJac4.2020-09-04 cd /hive/data/genomes/mm39/bed/lastzCalJac4.2020-09-04 printf '# mouse vs marmoset calJac4 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz BLASTZ_M=254 # TARGET: Mouse Mm39 SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: marmoset calJac4 SEQ2_DIR=/hive/data/genomes/calJac4/calJac4.2bit SEQ2_LEN=/hive/data/genomes/calJac4/chrom.sizes SEQ2_CHUNK=10000000 SEQ2_LIMIT=20 SEQ2_LAP=0 BASE=/hive/data/genomes/mm39/bed/lastzCalJac4.2020-09-04 TMPDIR=/dev/shm ' > DEF time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 & # real 269m7.515s cat fb.mm39.chainCalJac4Link.txt # 878425270 bases of 2654624157 (33.090%) in intersection cat fb.mm39.chainSynCalJac4Link.txt # 830808798 bases of 2654624157 (31.297%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev mm39 calJac4 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 342m45.296s cat fb.mm39.chainRBest.CalJac4.txt # 835984408 bases of 2654624157 (31.492%) in intersection mkdir /hive/data/genomes/calJac4/bed/blastz.mm39.swap cd /hive/data/genomes/calJac4/bed/blastz.mm39.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm39/bed/lastzCalJac4.2020-09-04/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 & # real 51m44.991s cat fb.calJac4.chainMm39Link.txt # 885334904 bases of 2859817025 (30.958%) in intersection cat fb.calJac4.chainSynMm39Link.txt # 831225065 bases of 2859817025 (29.066%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev calJac4 mm39 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 298m22.974s cat fb.calJac4.chainRBest.Mm39.txt # 834211414 bases of 2859817025 (29.170%) in intersection ############################################################################## # LASTZ Rat rn6 (DONE - 2020-10-20 - Hiram) mkdir /hive/data/genomes/mm39/bed/lastzRn6.2020-10-20 cd /hive/data/genomes/mm39/bed/lastzRn6.2020-10-20 printf '# rat vs mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse Mm39 SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: Rat Rn6 SEQ2_DIR=/hive/data/genomes/rn6/rn6.2bit SEQ2_LEN=/hive/data/genomes/rn6/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=500 BASE=/hive/data/genomes/mm39/bed/lastzRn6.2020-10-20 TMPDIR=/dev/shm ' > DEF # establish a screen to control this job screen -S mm39Rn6 time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 & # real 364m51.738s cat fb.mm39.chainRn6Link.txt # 1882154751 bases of 2654624157 (70.901%) in intersection cat fb.mm39.chainSynRn6Link.txt # 1758846483 bases of 2654624157 (66.256%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ mm39 rn6) > rbest.log 2>&1 & # real 580m33.404s cat fb.mm39.chainRBest.Rn6.txt # 1738608299 bases of 2654624157 (65.494%) in intersection mkdir /hive/data/genomes/rn6/bed/blastz.mm39.swap cd /hive/data/genomes/rn6/bed/blastz.mm39.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm39/bed/lastzRn6.2020-10-20/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1 # real 129m25.422s cat fb.rn6.chainMm39Link.txt # 1940254184 bases of 2729860805 (71.075%) in intersection cat fb.rn6.chainSynMm39Link.txt # 1808524707 bases of 2729860805 (66.250%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ rn6 mm39) > rbest.log 2>&1 # real 675m42.654s cat fb.rn6.chainRBest.Mm39.txt # 1740516499 bases of 2729860805 (63.758%) in intersection ############################################################################## # LASTZ Rhesus rheMac10 (DONE - 2020-10-20 - Hiram) mkdir /hive/data/genomes/mm39/bed/lastzRheMac10.2020-10-20 cd /hive/data/genomes/mm39/bed/lastzRheMac10.2020-10-20 printf '# rhesus vs mouse BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse Mm39 SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: Rhesus RheMac10 SEQ2_DIR=/hive/data/genomes/rheMac10/rheMac10.2bit SEQ2_LEN=/hive/data/genomes/rheMac10/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=500 BASE=/hive/data/genomes/mm39/bed/lastzRheMac10.2020-10-20 TMPDIR=/dev/shm ' > DEF # establish a screen to control this job screen -S mm39RheMac10 time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 & # real 243m13.015s cat fb.mm39.chainRheMac10Link.txt # 924807390 bases of 2654624157 (34.838%) in intersection cat fb.mm39.chainSynRheMac10Link.txt # 878558648 bases of 2654624157 (33.095%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ mm39 rheMac10) > rbest.log 2>&1 & # real 309m44.560s cat fb.mm39.chainRBest.RheMac10.txt # 880466873 bases of 2654624157 (33.167%) in intersection mkdir /hive/data/genomes/rheMac10/bed/blastz.mm39.swap cd /hive/data/genomes/rheMac10/bed/blastz.mm39.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm39/bed/lastzRheMac10.2020-10-20/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 # real 51m43.176s cat fb.rheMac10.chainMm39Link.txt # 920110067 bases of 2936892733 (31.329%) in intersection cat fb.rheMac10.chainSynMm39Link.txt # 876443625 bases of 2936892733 (29.843%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ rheMac10 mm39) > rbest.log 2>&1 # real 255m21.492s cat fb.rheMac10.chainRBest.Mm39.txt # 879043885 bases of 2936892733 (29.931%) in intersection -######################################################################### +############################################################################## +# LASTZ Rat rn7 (DONE - 2021-02-04 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzRn7.2021-02-04 + cd /hive/data/genomes/mm39/bed/lastzRn7.2021-02-04 + + printf '# rat vs mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Rat Rn7 +SEQ2_DIR=/hive/data/genomes/rn7/rn7.2bit +SEQ2_LEN=/hive/data/genomes/rn7/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=500 + +BASE=/hive/data/genomes/mm39/bed/lastzRn7.2021-02-04 +TMPDIR=/dev/shm +' > DEF + + # establish a screen to control this job + screen -S mm39Rn7 + time (doBlastzChainNet.pl -verbose=2 `pwd`/DEF \ + -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=medium) > do.log 2>&1 & + # real 364m51.738s + + sed -e 's/^/ # /;' fb.mm39.chainRn7Link.txt + # 1898735724 bases of 2654624157 (71.526%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynRn7Link.txt + # 1787593557 bases of 2654624157 (67.339%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 rn7) > rbest.log 2>&1 & +XXX - running - Fri Feb 5 11:01:26 PST 2021 + # real 580m33.404s + sed -e 's/^/ # /;' fb.mm39.chainRBest.Rn7.txt + # 1738608299 bases of 2654624157 (65.494%) in intersection + + mkdir /hive/data/genomes/rn7/bed/blastz.mm39.swap + cd /hive/data/genomes/rn7/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzRn7.2021-02-04/DEF \ + -swap -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=medium) > swap.log 2>&1 + # real 116m47.862s + + sed -e 's/^/ # /;' fb.rn7.chainMm39Link.txt + # 1855165978 bases of 2626580772 (70.630%) in intersection + sed -e 's/^/ # /;' fb.rn7.chainSynMm39Link.txt + # 1763550257 bases of 2626580772 (67.142%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + rn7 mm39) > rbest.log 2>&1 +XXX - running - Fri Feb 5 11:00:02 PST 2021 + # real 675m42.654s + + sed -e 's/^/ # /;' fb.rn7.chainRBest.Mm39.txt + # 1740516499 bases of 2729860805 (63.758%) in intersection + +############################################################################## +# LASTZ Chinese hamster criGriChoV2 (DONE - 2020-11-23 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzCriGriChoV2.2020-11-23 + cd /hive/data/genomes/mm39/bed/lastzCriGriChoV2.2020-11-23 + + printf '# Chinese hamster vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Chinese hamster CriGriChoV2 +SEQ2_DIR=/hive/data/genomes/criGriChoV2/criGriChoV2.2bit +SEQ2_LEN=/hive/data/genomes/criGriChoV2/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzCriGriChoV2.2020-11-23 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 458m24.193s + + sed -e 's/^/ #/;' fb.mm39.chainCriGriChoV2Link.txt + # 1587256983 bases of 2654624157 (59.792%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynCriGriChoV2Link.txt + # 1476080544 bases of 2654624157 (55.604%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 criGriChoV2) > rbest.log 2>&1 + # real 593m38.879s + + sed -e's/^/ #/;' fb.mm39.chainRBest.CriGriChoV2.txt + # 1452642485 bases of 2654624157 (54.721%) in intersection + + mkdir /hive/data/genomes/criGriChoV2/bed/blastz.mm39.swap + cd /hive/data/genomes/criGriChoV2/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzCriGriChoV2.2020-11-23/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 122m5.549s + + sed -e 's/^/ #/;' fb.criGriChoV2.chainMm39Link.txt + # 1610424504 bases of 2323924942 (69.298%) in intersection + sed -e 's/^/ #/;' fb.criGriChoV2.chainSynMm39Link.txt + # 1444363698 bases of 2323924942 (62.152%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + criGriChoV2 mm39) > rbest.log 2>&1 + # real 675m33.754s + + sed -e 's/^/ #/;' fb.criGriChoV2.chainRBest.Mm39.txt + # 1454060577 bases of 2323924942 (62.569%) in intersection + +############################################################################## +# LASTZ Beaver casCan1 (DONE - 2020-11-23 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzCasCan1.2020-11-23 + cd /hive/data/genomes/mm39/bed/lastzCasCan1.2020-11-23 + + printf '# Beaver vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Beaver CasCan1 +SEQ2_DIR=/hive/data/genomes/casCan1/casCan1.2bit +SEQ2_LEN=/hive/data/genomes/casCan1/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzCasCan1.2020-11-23 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 391m42.423s + + sed -e 's/^/ #/;' fb.mm39.chainCasCan1Link.txt + # 971598688 bases of 2654624157 (36.600%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynCasCan1Link.txt + # 860197979 bases of 2654624157 (32.404%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 casCan1) > rbest.log 2>&1 + # real 309m3.360s + + sed -e's/^/ #/;' fb.mm39.chainRBest.CasCan1.txt + # 913365652 bases of 2654624157 (34.407%) in intersection + + mkdir /hive/data/genomes/casCan1/bed/blastz.mm39.swap + cd /hive/data/genomes/casCan1/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzCasCan1.2020-11-23/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 69m39.719s + + sed -e 's/^/ #/;' fb.casCan1.chainMm39Link.txt + # 1030326326 bases of 2517974654 (40.919%) in intersection + sed -e 's/^/ #/;' fb.casCan1.chainSynMm39Link.txt + # 877942655 bases of 2517974654 (34.867%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + casCan1 mm39) > rbest.log 2>&1 + # real 342m21.552s + + sed -e 's/^/ #/;' fb.casCan1.chainRBest.Mm39.txt + # 912616046 bases of 2517974654 (36.244%) in intersection + +############################################################################## +# LASTZ Chinese pangolin manPen1 (DONE - 2020-11-23 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzManPen1.2020-11-23 + cd /hive/data/genomes/mm39/bed/lastzManPen1.2020-11-23 + + printf '# Chinese pangolin vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Chinese pangolin ManPen1 +SEQ2_DIR=/hive/data/genomes/manPen1/manPen1.2bit +SEQ2_LEN=/hive/data/genomes/manPen1/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=500 + +BASE=/hive/data/genomes/mm39/bed/lastzManPen1.2020-11-23 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 307m16.259s + + sed -e 's/^/ #/;' fb.mm39.chainManPen1Link.txt + # 725290847 bases of 2654624157 (27.322%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynManPen1Link.txt + # 600536473 bases of 2654624157 (22.622%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 manPen1) > rbest.log 2>&1 + # real 254m19.570s + + sed -e's/^/ #/;' fb.mm39.chainRBest.ManPen1.txt + # 686132793 bases of 2654624157 (25.847%) in intersection + + mkdir /hive/data/genomes/manPen1/bed/blastz.mm39.swap + cd /hive/data/genomes/manPen1/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzManPen1.2020-11-23/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 57m14.273s + + sed -e 's/^/ #/;' fb.manPen1.chainMm39Link.txt + # 711536446 bases of 1999066070 (35.593%) in intersection + sed -e 's/^/ #/;' fb.manPen1.chainSynMm39Link.txt + # 600806601 bases of 1999066070 (30.054%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + manPen1 mm39) > rbest.log 2>&1 + # real 258m8.812s + + sed -e 's/^/ #/;' fb.manPen1.chainRBest.Mm39.txt + # 685854051 bases of 1999066070 (34.309%) in intersection + +############################################################################## +# LASTZ Malayan flying lemur galVar1 (DONE - 2020-11-23 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzGalVar1.2020-11-23 + cd /hive/data/genomes/mm39/bed/lastzGalVar1.2020-11-23 + + printf '# Malayan flying lemur vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Malayan flying lemur GalVar1 +SEQ2_DIR=/hive/data/genomes/galVar1/galVar1.2bit +SEQ2_LEN=/hive/data/genomes/galVar1/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=500 + +BASE=/hive/data/genomes/mm39/bed/lastzGalVar1.2020-11-23 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 409m27.010s + + sed -e 's/^/ #/;' fb.mm39.chainGalVar1Link.txt + # 948074394 bases of 2654624157 (35.714%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynGalVar1Link.txt + # 833172992 bases of 2654624157 (31.386%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 galVar1) > rbest.log 2>&1 + # real 355m41.194s + + sed -e's/^/ #/;' fb.mm39.chainRBest.GalVar1.txt + # 895962299 bases of 2654624157 (33.751%) in intersection + + mkdir /hive/data/genomes/galVar1/bed/blastz.mm39.swap + cd /hive/data/genomes/galVar1/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzGalVar1.2020-11-23/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 113m39.933s + + sed -e 's/^/ #/;' fb.galVar1.chainMm39Link.txt + # 1013311093 bases of 2802917674 (36.152%) in intersection + sed -e 's/^/ #/;' fb.galVar1.chainSynMm39Link.txt + # 857584853 bases of 2802917674 (30.596%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + galVar1 mm39) > rbest.log 2>&1 + # real 412m23.326s + + sed -e 's/^/ #/;' fb.galVar1.chainRBest.Mm39.txt + # 894445877 bases of 2802917674 (31.911%) in intersection + +############################################################################## +# LASTZ Gorilla gorGor6 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzGorGor6.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzGorGor6.2020-11-24 + + printf '# Gorilla vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Gorilla GorGor6 +SEQ2_DIR=/hive/data/genomes/gorGor6/gorGor6.2bit +SEQ2_LEN=/hive/data/genomes/gorGor6/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzGorGor6.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 298m31.850s + + sed -e 's/^/ #/;' fb.mm39.chainGorGor6Link.txt + # 930815279 bases of 2654624157 (35.064%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynGorGor6Link.txt + # 882010048 bases of 2654624157 (33.225%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 gorGor6) > rbest.log 2>&1 + # real 302m25.603s + + sed -e's/^/ #/;' fb.mm39.chainRBest.GorGor6.txt + # 885577700 bases of 2654624157 (33.360%) in intersection + + mkdir /hive/data/genomes/gorGor6/bed/blastz.mm39.swap + cd /hive/data/genomes/gorGor6/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzGorGor6.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 56m58.641s + + sed -e 's/^/ #/;' fb.gorGor6.chainMm39Link.txt + # 1021664774 bases of 2999027915 (34.067%) in intersection + sed -e 's/^/ #/;' fb.gorGor6.chainSynMm39Link.txt + # 881068629 bases of 2999027915 (29.378%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + gorGor6 mm39) > rbest.log 2>&1 + # real 263m46.802s + + sed -e 's/^/ #/;' fb.gorGor6.chainRBest.Mm39.txt + # 884060521 bases of 2999027915 (29.478%) in intersection + +# ERROR: can not find hg38 vs. mm39 /DEF +############################################################################## +# LASTZ Bonobo panPan3 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzPanPan3.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzPanPan3.2020-11-24 + + printf '# Bonobo vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Bonobo PanPan3 +SEQ2_DIR=/hive/data/genomes/panPan3/panPan3.2bit +SEQ2_LEN=/hive/data/genomes/panPan3/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzPanPan3.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 314m48.787s + + sed -e 's/^/ #/;' fb.mm39.chainPanPan3Link.txt + # 936595620 bases of 2654624157 (35.282%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynPanPan3Link.txt + # 889095516 bases of 2654624157 (33.492%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 panPan3) > rbest.log 2>&1 + # real 315m43.802s + + sed -e's/^/ #/;' fb.mm39.chainRBest.PanPan3.txt + # 891388431 bases of 2654624157 (33.579%) in intersection + + mkdir /hive/data/genomes/panPan3/bed/blastz.mm39.swap + cd /hive/data/genomes/panPan3/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzPanPan3.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 55m37.718s + + sed -e 's/^/ #/;' fb.panPan3.chainMm39Link.txt + # 1022366328 bases of 3015350297 (33.905%) in intersection + sed -e 's/^/ #/;' fb.panPan3.chainSynMm39Link.txt + # 888141375 bases of 3015350297 (29.454%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + panPan3 mm39) > rbest.log 2>&1 + # real 275m25.911s + + sed -e 's/^/ #/;' fb.panPan3.chainRBest.Mm39.txt + # 889786782 bases of 3015350297 (29.509%) in intersection + +############################################################################## +# LASTZ Chimp panTro6 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzPanTro6.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzPanTro6.2020-11-24 + + printf '# Chimp vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Chimp PanTro6 +SEQ2_DIR=/hive/data/genomes/panTro6/panTro6.2bit +SEQ2_LEN=/hive/data/genomes/panTro6/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzPanTro6.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 292m55.308s + + sed -e 's/^/ #/;' fb.mm39.chainPanTro6Link.txt + # 936842603 bases of 2654624157 (35.291%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynPanTro6Link.txt + # 889591386 bases of 2654624157 (33.511%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 panTro6) > rbest.log 2>&1 + # real 318m39.695s + + sed -e's/^/ #/;' fb.mm39.chainRBest.PanTro6.txt + # 892161322 bases of 2654624157 (33.608%) in intersection + + mkdir /hive/data/genomes/panTro6/bed/blastz.mm39.swap + cd /hive/data/genomes/panTro6/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzPanTro6.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 54m39.744s + + sed -e 's/^/ #/;' fb.panTro6.chainMm39Link.txt + # 936830473 bases of 3018592990 (31.035%) in intersection + sed -e 's/^/ #/;' fb.panTro6.chainSynMm39Link.txt + # 890135394 bases of 3018592990 (29.488%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + panTro6 mm39) > rbest.log 2>&1 + # real 272m44.051s + + sed -e 's/^/ #/;' fb.panTro6.chainRBest.Mm39.txt + # 890578770 bases of 3018592990 (29.503%) in intersection + +############################################################################## +# LASTZ Tarsier tarSyr2 (DONE - 2020-11-23 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzTarSyr2.2020-11-23 + cd /hive/data/genomes/mm39/bed/lastzTarSyr2.2020-11-23 + + printf '# Tarsier vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Tarsier TarSyr2 +SEQ2_DIR=/hive/data/genomes/tarSyr2/tarSyr2.2bit +SEQ2_LEN=/hive/data/genomes/tarSyr2/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=500 + +BASE=/hive/data/genomes/mm39/bed/lastzTarSyr2.2020-11-23 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 209m1.579s +real 235m21.878s + + sed -e 's/^/ #/;' fb.mm39.chainTarSyr2Link.txt + # 856869221 bases of 2654624157 (32.278%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynTarSyr2Link.txt + # 767407640 bases of 2654624157 (28.908%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 tarSyr2) > rbest.log 2>&1 + # real 235m21.816s + + sed -e's/^/ #/;' fb.mm39.chainRBest.TarSyr2.txt + # 813072686 bases of 2654624157 (30.629%) in intersection + + mkdir /hive/data/genomes/tarSyr2/bed/blastz.mm39.swap + cd /hive/data/genomes/tarSyr2/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzTarSyr2.2020-11-23/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 138m17.406s + + sed -e 's/^/ #/;' fb.tarSyr2.chainMm39Link.txt + # 901691832 bases of 3405755564 (26.476%) in intersection + sed -e 's/^/ #/;' fb.tarSyr2.chainSynMm39Link.txt + # 771115772 bases of 3405755564 (22.642%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + tarSyr2 mm39) > rbest.log 2>&1 + # + + sed -e 's/^/ #/;' fb.tarSyr2.chainRBest.Mm39.txt +############################################################################## +# LASTZ Bushbaby otoGar3 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzOtoGar3.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzOtoGar3.2020-11-24 + + printf '# Bushbaby vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Bushbaby OtoGar3 +SEQ2_DIR=/hive/data/genomes/otoGar3/otoGar3.2bit +SEQ2_LEN=/hive/data/genomes/otoGar3/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzOtoGar3.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 397m59.255s + + sed -e 's/^/ #/;' fb.mm39.chainOtoGar3Link.txt + # 789200353 bases of 2654624157 (29.729%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynOtoGar3Link.txt + # 740066864 bases of 2654624157 (27.878%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 otoGar3) > rbest.log 2>&1 + # real 188m39.612s + + sed -e's/^/ #/;' fb.mm39.chainRBest.OtoGar3.txt + # 750275917 bases of 2654624157 (28.263%) in intersection + + mkdir /hive/data/genomes/otoGar3/bed/blastz.mm39.swap + cd /hive/data/genomes/otoGar3/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzOtoGar3.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 45m14.239s + + sed -e 's/^/ #/;' fb.otoGar3.chainMm39Link.txt + # 776190961 bases of 2359530453 (32.896%) in intersection + sed -e 's/^/ #/;' fb.otoGar3.chainSynMm39Link.txt + # 734606528 bases of 2359530453 (31.134%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + otoGar3 mm39) > rbest.log 2>&1 + # real 166m37.534s + + sed -e 's/^/ #/;' fb.otoGar3.chainRBest.Mm39.txt + # 749239900 bases of 2359530453 (31.754%) in intersection + +############################################################################## +# LASTZ Horse equCab3 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzEquCab3.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzEquCab3.2020-11-24 + + printf '# Horse vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Horse EquCab3 +SEQ2_DIR=/hive/data/genomes/equCab3/equCab3.2bit +SEQ2_LEN=/hive/data/genomes/equCab3/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzEquCab3.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 406m37.315s + + sed -e 's/^/ #/;' fb.mm39.chainEquCab3Link.txt + # 924631395 bases of 2654624157 (34.831%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynEquCab3Link.txt + # 877123772 bases of 2654624157 (33.041%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 equCab3) > rbest.log 2>&1 + # real 247m56.186s + + sed -e's/^/ #/;' fb.mm39.chainRBest.EquCab3.txt + # 878079495 bases of 2654624157 (33.077%) in intersection + + mkdir /hive/data/genomes/equCab3/bed/blastz.mm39.swap + cd /hive/data/genomes/equCab3/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzEquCab3.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 60m58.831s + + sed -e 's/^/ #/;' fb.equCab3.chainMm39Link.txt + # 933513515 bases of 2497530654 (37.377%) in intersection + sed -e 's/^/ #/;' fb.equCab3.chainSynMm39Link.txt + # 897517908 bases of 2497530654 (35.936%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + equCab3 mm39) > rbest.log 2>&1 + # real 185m17.962s + + sed -e 's/^/ #/;' fb.equCab3.chainRBest.Mm39.txt + # 876632896 bases of 2497530654 (35.100%) in intersection + +############################################################################## +# LASTZ Dolphin turTru2 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzTurTru2.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzTurTru2.2020-11-24 + + printf '# Dolphin vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Dolphin TurTru2 +SEQ2_DIR=/hive/data/genomes/turTru2/turTru2.2bit +SEQ2_LEN=/hive/data/genomes/turTru2/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=500 + +BASE=/hive/data/genomes/mm39/bed/lastzTurTru2.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 391m42.619s + + sed -e 's/^/ #/;' fb.mm39.chainTurTru2Link.txt + # 801389023 bases of 2654624157 (30.188%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynTurTru2Link.txt + # 661029305 bases of 2654624157 (24.901%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 turTru2) > rbest.log 2>&1 + # real 315m15.793s + + sed -e's/^/ #/;' fb.mm39.chainRBest.TurTru2.txt + # 763697442 bases of 2654624157 (28.769%) in intersection + + mkdir /hive/data/genomes/turTru2/bed/blastz.mm39.swap + cd /hive/data/genomes/turTru2/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzTurTru2.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 86m10.671s + + sed -e 's/^/ #/;' fb.turTru2.chainMm39Link.txt + # 780128552 bases of 2332402443 (33.447%) in intersection + sed -e 's/^/ #/;' fb.turTru2.chainSynMm39Link.txt + # 660604333 bases of 2332402443 (28.323%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + turTru2 mm39) > rbest.log 2>&1 + # real 344m38.287s + + sed -e 's/^/ #/;' fb.turTru2.chainRBest.Mm39.txt + # 763173700 bases of 2332402443 (32.720%) in intersection + +############################################################################## +# LASTZ Dog canFam4 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzCanFam4.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzCanFam4.2020-11-24 + + printf '# Dog vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Dog CanFam4 +SEQ2_DIR=/hive/data/genomes/canFam4/canFam4.2bit +SEQ2_LEN=/hive/data/genomes/canFam4/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzCanFam4.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 394m53.229s + + sed -e 's/^/ #/;' fb.mm39.chainCanFam4Link.txt + # 779819643 bases of 2654624157 (29.376%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynCanFam4Link.txt + # 736821453 bases of 2654624157 (27.756%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 canFam4) > rbest.log 2>&1 + # real 220m48.500s + + sed -e's/^/ #/;' fb.mm39.chainRBest.CanFam4.txt + # 742006400 bases of 2654624157 (27.951%) in intersection + + mkdir /hive/data/genomes/canFam4/bed/blastz.mm39.swap + cd /hive/data/genomes/canFam4/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzCanFam4.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 50m2.866s + + sed -e 's/^/ #/;' fb.canFam4.chainMm39Link.txt + # 775644736 bases of 2481941580 (31.252%) in intersection + sed -e 's/^/ #/;' fb.canFam4.chainSynMm39Link.txt + # 738180386 bases of 2481941580 (29.742%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + canFam4 mm39) > rbest.log 2>&1 + # real 184m49.168s + + sed -e 's/^/ #/;' fb.canFam4.chainRBest.Mm39.txt + # 740879439 bases of 2481941580 (29.851%) in intersection + +############################################################################## +# LASTZ Pig susScr3 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzSusScr3.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzSusScr3.2020-11-24 + + printf '# Pig vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Pig SusScr3 +SEQ2_DIR=/hive/data/genomes/susScr3/susScr3.2bit +SEQ2_LEN=/hive/data/genomes/susScr3/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzSusScr3.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 392m59.025s + + sed -e 's/^/ #/;' fb.mm39.chainSusScr3Link.txt + # 679873302 bases of 2654624157 (25.611%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynSusScr3Link.txt + # 617246479 bases of 2654624157 (23.252%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 susScr3) > rbest.log 2>&1 + # real 354m58.989s + + sed -e's/^/ #/;' fb.mm39.chainRBest.SusScr3.txt + # 644866009 bases of 2654624157 (24.292%) in intersection + + mkdir /hive/data/genomes/susScr3/bed/blastz.mm39.swap + cd /hive/data/genomes/susScr3/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzSusScr3.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 42m7.986s + + sed -e 's/^/ #/;' fb.susScr3.chainMm39Link.txt + # 742566440 bases of 2525294057 (29.405%) in intersection + sed -e 's/^/ #/;' fb.susScr3.chainSynMm39Link.txt + # 695214883 bases of 2525294057 (27.530%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + susScr3 mm39) > rbest.log 2>&1 + # real 317m19.244s + + sed -e 's/^/ #/;' fb.susScr3.chainRBest.Mm39.txt + # 644557808 bases of 2525294057 (25.524%) in intersection + +############################################################################## +# LASTZ Elephant loxAfr3 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzLoxAfr3.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzLoxAfr3.2020-11-24 + + printf '# Elephant vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Elephant LoxAfr3 +SEQ2_DIR=/hive/data/genomes/loxAfr3/loxAfr3.2bit +SEQ2_LEN=/hive/data/genomes/loxAfr3/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzLoxAfr3.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 644m59.241s + + sed -e 's/^/ #/;' fb.mm39.chainLoxAfr3Link.txt + # 683720656 bases of 2654624157 (25.756%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynLoxAfr3Link.txt + # 632517819 bases of 2654624157 (23.827%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 loxAfr3) > rbest.log 2>&1 + # real 212m39.008s + + sed -e's/^/ #/;' fb.mm39.chainRBest.LoxAfr3.txt + # 648164944 bases of 2654624157 (24.416%) in intersection + + mkdir /hive/data/genomes/loxAfr3/bed/blastz.mm39.swap + cd /hive/data/genomes/loxAfr3/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzLoxAfr3.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 48m31.606s + + sed -e 's/^/ #/;' fb.loxAfr3.chainMm39Link.txt + # 673050238 bases of 3118565340 (21.582%) in intersection + sed -e 's/^/ #/;' fb.loxAfr3.chainSynMm39Link.txt + # 630456477 bases of 3118565340 (20.216%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + loxAfr3 mm39) > rbest.log 2>&1 + # real 181m46.370s + + sed -e 's/^/ #/;' fb.loxAfr3.chainRBest.Mm39.txt + # 647633378 bases of 3118565340 (20.767%) in intersection + +############################################################################## +# LASTZ Rabbit oryCun2 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzOryCun2.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzOryCun2.2020-11-24 + + printf '# Rabbit vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Rabbit OryCun2 +SEQ2_DIR=/hive/data/genomes/oryCun2/oryCun2.2bit +SEQ2_LEN=/hive/data/genomes/oryCun2/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzOryCun2.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 549m40.618s + + sed -e 's/^/ #/;' fb.mm39.chainOryCun2Link.txt + # 668479596 bases of 2654624157 (25.182%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynOryCun2Link.txt + # 612665047 bases of 2654624157 (23.079%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 oryCun2) > rbest.log 2>&1 + # real 315m53.451s + + sed -e's/^/ #/;' fb.mm39.chainRBest.OryCun2.txt + # 631190305 bases of 2654624157 (23.777%) in intersection + + mkdir /hive/data/genomes/oryCun2/bed/blastz.mm39.swap + cd /hive/data/genomes/oryCun2/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzOryCun2.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 40m58.805s + + sed -e 's/^/ #/;' fb.oryCun2.chainMm39Link.txt + # 668039169 bases of 2604023284 (25.654%) in intersection + sed -e 's/^/ #/;' fb.oryCun2.chainSynMm39Link.txt + # 610356040 bases of 2604023284 (23.439%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + oryCun2 mm39) > rbest.log 2>&1 + # real 308m22.599s + + sed -e 's/^/ #/;' fb.oryCun2.chainRBest.Mm39.txt + # 630726758 bases of 2604023284 (24.221%) in intersection + +############################################################################## +# LASTZ Sheep oviAri4 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzOviAri4.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzOviAri4.2020-11-24 + + printf '# Sheep vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Sheep OviAri4 +SEQ2_DIR=/hive/data/genomes/oviAri4/oviAri4.2bit +SEQ2_LEN=/hive/data/genomes/oviAri4/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzOviAri4.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 558m13.976s + + sed -e 's/^/ #/;' fb.mm39.chainOviAri4Link.txt + # 695514891 bases of 2654624157 (26.200%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynOviAri4Link.txt + # 646653235 bases of 2654624157 (24.360%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 oviAri4) > rbest.log 2>&1 + # real 285m33.374s + + sed -e's/^/ #/;' fb.mm39.chainRBest.OviAri4.txt + # 657902325 bases of 2654624157 (24.783%) in intersection + + mkdir /hive/data/genomes/oviAri4/bed/blastz.mm39.swap + cd /hive/data/genomes/oviAri4/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzOviAri4.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 40m40.419s + + sed -e 's/^/ #/;' fb.oviAri4.chainMm39Link.txt + # 681813597 bases of 2587515673 (26.350%) in intersection + sed -e 's/^/ #/;' fb.oviAri4.chainSynMm39Link.txt + # 643966161 bases of 2587515673 (24.887%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + oviAri4 mm39) > rbest.log 2>&1 + # real 244m54.731s + + sed -e 's/^/ #/;' fb.oviAri4.chainRBest.Mm39.txt + # 657036323 bases of 2587515673 (25.393%) in intersection + +############################################################################## +# LASTZ Hawaiian monk seal neoSch1 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzNeoSch1.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzNeoSch1.2020-11-24 + + printf '# Hawaiian monk seal vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Hawaiian monk seal NeoSch1 +SEQ2_DIR=/hive/data/genomes/neoSch1/neoSch1.2bit +SEQ2_LEN=/hive/data/genomes/neoSch1/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzNeoSch1.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 528m58.199s + + sed -e 's/^/ #/;' fb.mm39.chainNeoSch1Link.txt + # 829753178 bases of 2654624157 (31.257%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynNeoSch1Link.txt + # 782537839 bases of 2654624157 (29.478%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 neoSch1) > rbest.log 2>&1 + # real 188m16.478s + + sed -e's/^/ #/;' fb.mm39.chainRBest.NeoSch1.txt + # 789218206 bases of 2654624157 (29.730%) in intersection + + mkdir /hive/data/genomes/neoSch1/bed/blastz.mm39.swap + cd /hive/data/genomes/neoSch1/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzNeoSch1.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 48m21.632s + + sed -e 's/^/ #/;' fb.neoSch1.chainMm39Link.txt + # 806278963 bases of 2347122535 (34.352%) in intersection + sed -e 's/^/ #/;' fb.neoSch1.chainSynMm39Link.txt + # 776403929 bases of 2347122535 (33.079%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + neoSch1 mm39) > rbest.log 2>&1 + # real 148m0.700s + + sed -e 's/^/ #/;' fb.neoSch1.chainRBest.Mm39.txt + # 788121681 bases of 2347122535 (33.578%) in intersection + +############################################################################## +# LASTZ Cow bosTau9 (DONE - 2020-11-23 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzBosTau9.2020-11-23 + cd /hive/data/genomes/mm39/bed/lastzBosTau9.2020-11-23 + + printf '# Cow vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Cow BosTau9 +SEQ2_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit +SEQ2_LEN=/hive/data/genomes/bosTau9/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzBosTau9.2020-11-23 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 174m47.736s + + sed -e 's/^/ #/;' fb.mm39.chainBosTau9Link.txt + # 705812203 bases of 2654624157 (26.588%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynBosTau9Link.txt + # 659578523 bases of 2654624157 (24.846%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 bosTau9) > rbest.log 2>&1 + # real 229m35.741s + + sed -e's/^/ #/;' fb.mm39.chainRBest.BosTau9.txt + # 668635567 bases of 2654624157 (25.188%) in intersection + + mkdir /hive/data/genomes/bosTau9/bed/blastz.mm39.swap + cd /hive/data/genomes/bosTau9/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzBosTau9.2020-11-23/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 40m50.213s + + sed -e 's/^/ #/;' fb.bosTau9.chainMm39Link.txt + # 697118681 bases of 2715853792 (25.668%) in intersection + sed -e 's/^/ #/;' fb.bosTau9.chainSynMm39Link.txt + # 661108066 bases of 2715853792 (24.343%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + bosTau9 mm39) > rbest.log 2>&1 + # real 194m20.003s + + sed -e 's/^/ #/;' fb.bosTau9.chainRBest.Mm39.txt + # 667741402 bases of 2715853792 (24.587%) in intersection + +############################################################################## +# LASTZ Hedgehog eriEur2 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzEriEur2.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzEriEur2.2020-11-24 + + printf '# Hedgehog vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Hedgehog EriEur2 +SEQ2_DIR=/hive/data/genomes/eriEur2/eriEur2.2bit +SEQ2_LEN=/hive/data/genomes/eriEur2/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzEriEur2.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 494m20.449s + + sed -e 's/^/ #/;' fb.mm39.chainEriEur2Link.txt + # 357042649 bases of 2654624157 (13.450%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynEriEur2Link.txt + # 252215223 bases of 2654624157 (9.501%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 eriEur2) > rbest.log 2>&1 + # real 289m12.956s + + sed -e's/^/ #/;' fb.mm39.chainRBest.EriEur2.txt + # 327119175 bases of 2654624157 (12.323%) in intersection + + mkdir /hive/data/genomes/eriEur2/bed/blastz.mm39.swap + cd /hive/data/genomes/eriEur2/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzEriEur2.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 24m29.084s + + sed -e 's/^/ #/;' fb.eriEur2.chainMm39Link.txt + # 345274697 bases of 2333073535 (14.799%) in intersection + sed -e 's/^/ #/;' fb.eriEur2.chainSynMm39Link.txt + # 251961733 bases of 2333073535 (10.800%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + eriEur2 mm39) > rbest.log 2>&1 + # real 275m16.464s + + sed -e 's/^/ #/;' fb.eriEur2.chainRBest.Mm39.txt + # 327058246 bases of 2333073535 (14.018%) in intersection + +############################################################################## +# LASTZ Tenrec echTel2 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzEchTel2.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzEchTel2.2020-11-24 + + printf '# Tenrec vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Tenrec EchTel2 +SEQ2_DIR=/hive/data/genomes/echTel2/echTel2.2bit +SEQ2_LEN=/hive/data/genomes/echTel2/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzEchTel2.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + # real 652m56.936s + + sed -e 's/^/ #/;' fb.mm39.chainEchTel2Link.txt + # 383749102 bases of 2654624157 (14.456%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynEchTel2Link.txt + # 296272244 bases of 2654624157 (11.161%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 echTel2) > rbest.log 2>&1 + # real 308m56.712s + + sed -e's/^/ #/;' fb.mm39.chainRBest.EchTel2.txt + # 353828423 bases of 2654624157 (13.329%) in intersection + + mkdir /hive/data/genomes/echTel2/bed/blastz.mm39.swap + cd /hive/data/genomes/echTel2/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzEchTel2.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + # real 26m3.037s + + sed -e 's/^/ #/;' fb.echTel2.chainMm39Link.txt + # 380081282 bases of 2605196361 (14.589%) in intersection + sed -e 's/^/ #/;' fb.echTel2.chainSynMm39Link.txt + # 295227610 bases of 2605196361 (11.332%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + echTel2 mm39) > rbest.log 2>&1 + # real 289m38.161s + + sed -e 's/^/ #/;' fb.echTel2.chainRBest.Mm39.txt + # 353819264 bases of 2605196361 (13.581%) in intersection + +############################################################################## +# LASTZ Opossum monDom5 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzMonDom5.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzMonDom5.2020-11-24 + + printf '# Opossum vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Opossum MonDom5 +SEQ2_DIR=/hive/data/genomes/monDom5/monDom5.2bit +SEQ2_LEN=/hive/data/genomes/monDom5/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzMonDom5.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + # real 393m28.801s + + sed -e 's/^/ #/;' fb.mm39.chainMonDom5Link.txt + # 142865188 bases of 2654624157 (5.382%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynMonDom5Link.txt + # 116528842 bases of 2654624157 (4.390%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 monDom5) > rbest.log 2>&1 + # real 317m52.699s + + sed -e's/^/ #/;' fb.mm39.chainRBest.MonDom5.txt + # 122836952 bases of 2654624157 (4.627%) in intersection + + mkdir /hive/data/genomes/monDom5/bed/blastz.mm39.swap + cd /hive/data/genomes/monDom5/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzMonDom5.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + # real 14m50.171s + + sed -e 's/^/ #/;' fb.monDom5.chainMm39Link.txt + # 141605466 bases of 3501660299 (4.044%) in intersection + sed -e 's/^/ #/;' fb.monDom5.chainSynMm39Link.txt + # 117256524 bases of 3501660299 (3.349%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + monDom5 mm39) > rbest.log 2>&1 + # real 293m57.633s + + sed -e 's/^/ #/;' fb.monDom5.chainRBest.Mm39.txt + # 123101776 bases of 3501660299 (3.516%) in intersection + +############################################################################## +# LASTZ X. tropicalis xenTro9 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzXenTro9.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzXenTro9.2020-11-24 + + printf '# X. tropicalis vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: X. tropicalis XenTro9 +SEQ2_DIR=/hive/data/genomes/xenTro9/xenTro9.2bit +SEQ2_LEN=/hive/data/genomes/xenTro9/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzXenTro9.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + # real 331m42.313s + + sed -e 's/^/ #/;' fb.mm39.chainXenTro9Link.txt + # 51383904 bases of 2654624157 (1.936%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynXenTro9Link.txt + # 20789787 bases of 2654624157 (0.783%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 xenTro9) > rbest.log 2>&1 + # real 140m2.922s + + sed -e's/^/ #/;' fb.mm39.chainRBest.XenTro9.txt + # 35952894 bases of 2654624157 (1.354%) in intersection + + mkdir /hive/data/genomes/xenTro9/bed/blastz.mm39.swap + cd /hive/data/genomes/xenTro9/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzXenTro9.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + # real 8m9.270s + + sed -e 's/^/ #/;' fb.xenTro9.chainMm39Link.txt + # 53364345 bases of 1369865365 (3.896%) in intersection + sed -e 's/^/ #/;' fb.xenTro9.chainSynMm39Link.txt + # 21157884 bases of 1369865365 (1.545%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + xenTro9 mm39) > rbest.log 2>&1 + # real 130m14.139s + + sed -e 's/^/ #/;' fb.xenTro9.chainRBest.Mm39.txt + # 35757239 bases of 1369865365 (2.610%) in intersection + +############################################################################## +# LASTZ Chicken galGal6 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzGalGal6.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzGalGal6.2020-11-24 + + printf '# Chicken vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Chicken GalGal6 +SEQ2_DIR=/hive/data/genomes/galGal6/galGal6.2bit +SEQ2_LEN=/hive/data/genomes/galGal6/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzGalGal6.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + # real 266m7.103s + + sed -e 's/^/ #/;' fb.mm39.chainGalGal6Link.txt + # 67356693 bases of 2654624157 (2.537%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynGalGal6Link.txt + # 48715227 bases of 2654624157 (1.835%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 galGal6) > rbest.log 2>&1 + # real 66m59.502s + + sed -e's/^/ #/;' fb.mm39.chainRBest.GalGal6.txt + # 53500116 bases of 2654624157 (2.015%) in intersection + + mkdir /hive/data/genomes/galGal6/bed/blastz.mm39.swap + cd /hive/data/genomes/galGal6/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzGalGal6.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + # real 4m26.280s + + sed -e 's/^/ #/;' fb.galGal6.chainMm39Link.txt + # 56760804 bases of 1055588482 (5.377%) in intersection + sed -e 's/^/ #/;' fb.galGal6.chainSynMm39Link.txt + # 48093000 bases of 1055588482 (4.556%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + galGal6 mm39) > rbest.log 2>&1 + # real 45m18.947s + + sed -e 's/^/ #/;' fb.galGal6.chainRBest.Mm39.txt + # 53410494 bases of 1055588482 (5.060%) in intersection + +############################################################################## +# LASTZ Lamprey petMar3 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzPetMar3.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzPetMar3.2020-11-24 + + printf '# Lamprey vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Lamprey PetMar3 +SEQ2_DIR=/hive/data/genomes/petMar3/petMar3.2bit +SEQ2_LEN=/hive/data/genomes/petMar3/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzPetMar3.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + # real 194m56.315s + + sed -e 's/^/ #/;' fb.mm39.chainPetMar3Link.txt + # 24028824 bases of 2654624157 (0.905%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynPetMar3Link.txt + # 726866 bases of 2654624157 (0.027%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 petMar3) > rbest.log 2>&1 + # real 82m40.621s + + sed -e's/^/ #/;' fb.mm39.chainRBest.PetMar3.txt + # 13736315 bases of 2654624157 (0.517%) in intersection + + mkdir /hive/data/genomes/petMar3/bed/blastz.mm39.swap + cd /hive/data/genomes/petMar3/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzPetMar3.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + # real 3m0.468s + + sed -e 's/^/ #/;' fb.petMar3.chainMm39Link.txt + # 22633976 bases of 1043181598 (2.170%) in intersection + sed -e 's/^/ #/;' fb.petMar3.chainSynMm39Link.txt + # 729652 bases of 1043181598 (0.070%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + petMar3 mm39) > rbest.log 2>&1 + # real 75m38.286s + + sed -e 's/^/ #/;' fb.petMar3.chainRBest.Mm39.txt + # 13597551 bases of 1043181598 (1.303%) in intersection + +############################################################################## +# LASTZ Zebrafish danRer11 (DONE - 2020-11-24 - Hiram) + mkdir /hive/data/genomes/mm39/bed/lastzDanRer11.2020-11-24 + cd /hive/data/genomes/mm39/bed/lastzDanRer11.2020-11-24 + + printf '# Zebrafish vs Mouse +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz +# TARGET: Mouse Mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 + +# QUERY: Zebrafish DanRer11 +SEQ2_DIR=/hive/data/genomes/danRer11/danRer11.2bit +SEQ2_LEN=/hive/data/genomes/danRer11/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzDanRer11.2020-11-24 +TMPDIR=/dev/shm +' > DEF + + time (doBlastzChainNet.pl -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + # real 311m5.559s + + sed -e 's/^/ #/;' fb.mm39.chainDanRer11Link.txt + # 37601772 bases of 2654624157 (1.416%) in intersection + sed -e 's/^/ #/;' fb.mm39.chainSynDanRer11Link.txt + # 4901291 bases of 2654624157 (0.185%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + mm39 danRer11) > rbest.log 2>&1 + # real 105m41.096s + + sed -e's/^/ #/;' fb.mm39.chainRBest.DanRer11.txt + # 25140390 bases of 2654624157 (0.947%) in intersection + + mkdir /hive/data/genomes/danRer11/bed/blastz.mm39.swap + cd /hive/data/genomes/danRer11/bed/blastz.mm39.swap + time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ + /hive/data/genomes/mm39/bed/lastzDanRer11.2020-11-24/DEF \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + # real 4m19.907s + + sed -e 's/^/ #/;' fb.danRer11.chainMm39Link.txt + # 46907638 bases of 1674677181 (2.801%) in intersection + sed -e 's/^/ #/;' fb.danRer11.chainSynMm39Link.txt + # 6476709 bases of 1674677181 (0.387%) in intersection + + time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ + danRer11 mm39) > rbest.log 2>&1 + # real 96m59.148s + + sed -e 's/^/ #/;' fb.danRer11.chainRBest.Mm39.txt + # 25019759 bases of 1674677181 (1.494%) in intersection + +##############################################################################