d6045f07a6bd4aa42e2b415b97f043977a425944 gperez2 Sun Jul 30 23:48:02 2023 -0700 mm39 vs. GCA_001624445.1 lastz/chain/net run for user, refs #31040 diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt index 682cfdf..8c709ba 100644 --- src/hg/makeDb/doc/mm39/lastzRuns.txt +++ src/hg/makeDb/doc/mm39/lastzRuns.txt @@ -1,2601 +1,2683 @@ ############################################################################## # 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 & # real 588m38.122s sed -e 's/^/ # /;' fb.mm39.chainRBest.Rn7.txt # 1754204799 bases of 2654624157 (66.081%) 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 # real 605m42.354s sed -e 's/^/ # /;' fb.rn7.chainRBest.Mm39.txt # 1754416686 bases of 2626580772 (66.795%) 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 ############################################################################## # LASTZ American beaver GCF_001984765.1 (DONE - 2021-01-22 - Hiram) mkdir /hive/data/genomes/mm39/bed/lastzGCF_001984765.1.2021-01-22 cd /hive/data/genomes/mm39/bed/lastzGCF_001984765.1.2021-01-22 printf '# GCF_001984765.1 vs mm39 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: American beaver GCF_001984765.1 # GCF/001/984/765/GCF_001984765.1_C.can_genome_v1.0 # should be the same as casCan1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/001/984/765/GCF_001984765.1/GCF_001984765.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/001/984/765/GCF_001984765.1/GCF_001984765.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm39/bed/lastzGCF_001984765.1.2021-01-22 TMPDIR=/dev/shm ' > DEF export targetDb="mm39" export asmId="GCF_001984765.1" export accessionId="${asmId}_C.can_genome_v1.0" export gcPath="GCF/001/984/765" cd /hive/data/genomes/${targetDb}/bed/lastz${asmId}.2021-01-22 time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 159m54.416s sed -e 's/^/ # /;' fb.$targetDb.chain.${asmId}Link.txt # 965922133 bases of 2728222451 (35.405%) in intersection sed -e 's/^/ # /;' fb.$targetDb.chainSyn.${asmId}Link.txt # 861770999 bases of 2728222451 (31.587%) in intersection time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \ -querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \ $targetDb ${asmId}) >> rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 308m15.730s sed -e 's/^/ # /;' fb.$targetDb.chainRBest.$asmId.txt # 913563482 bases of 2728222451 (33.486%) in intersection # real 468m10.166s total time all of above export target="mm39" export Target="Mm39" export query="GCF_001984765.1" export asmId="GCF_001984765.1_C.can_genome_v1.0" export gcPath="GCF/001/984/765" mkdir /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap cd /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 -swapDir=`pwd` \ /hive/data/genomes/${target}/bed/lastz.${query}/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -swap -chainMinScore=3000 -chainLinearGap=medium) >> swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 70m57.610s sed -e 's/^/ # /;' fb.${query}.chain.${Target}Link.txt # 1021869459 bases of 2518306565 (40.578%) in intersection sed -e 's/^/ # /;' fb.${query}.chainSyn.${Target}Link.txt # 879061651 bases of 2518306565 (34.907%) in intersection time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \ $query $target) >> rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 294m45.010s sed -e 's/^/ # /;' fb.${query}.chainRBest.${Target}.txt # 913513030 bases of 2518306565 (36.275%) in intersection ############################################################################## # LASTZ lance-tailed manakin GCF_009829145.1 (DONE - 2020-11-24 - Hiram) mkdir /hive/data/genomes/mm39/bed/lastzGCF_009829145.1.2020-11-24 cd /hive/data/genomes/mm39/bed/lastzGCF_009829145.1.2020-11-24 printf '# GCF_009829145.1 vs mm39 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse Mm39 SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: lance-tailed manakin GCF_009829145.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/009/829/145/GCF_009829145.1/GCF_009829145.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/009/829/145/GCF_009829145.1/GCF_009829145.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm39/bed/lastzGCF_009829145.1.2020-11-24 TMPDIR=/dev/shm ' > DEF export targetDb="mm39" export asmId="GCF_009829145.1" export accessionId="${asmId}_bChiLan1.pri" export gcPath="GCF/009/829/145" cd /hive/data/genomes/${targetDb}/bed/lastz${asmId}.2020-11-24 time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 159m54.416s missed this measurement sed -e 's/^/ # /;' fb.$targetDb.chain.${asmId}Link.txt # 67418947 bases of 2728222451 (2.471%) in intersection sed -e 's/^/ # /;' fb.$targetDb.chainSyn.${asmId}Link.txt # 12681011 bases of 2728222451 (0.465%) in intersection time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \ -querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \ $targetDb ${asmId}) >> rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 323m14.591s sed -e 's/^/ # /;' fb.$targetDb.chainRBest.$asmId.txt # 52282223 bases of 2728222451 (1.916%) in intersection export target="mm39" export Target="Mm39" export query="GCF_009829145.1" export asmId="GCF_009829145.1_bChiLan1.pri" export gcPath="GCF/009/829/145" mkdir /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap cd /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 -swapDir=`pwd` \ /hive/data/genomes/${target}/bed/lastz.${query}/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -swap -chainMinScore=3000 -chainLinearGap=medium) >> swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 5m33.993s sed -e 's/^/ # /;' fb.${query}.chain.${Target}Link.txt # 56730326 bases of 1089631598 (5.206%) in intersection sed -e 's/^/ # /;' fb.${query}.chainSyn.${Target}Link.txt # 12678262 bases of 1089631598 (1.164%) in intersection time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \ $query $target) >> rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 288m55.058s sed -e 's/^/ # /;' fb.${query}.chainRBest.${Target}.txt # 51851922 bases of 1089631598 (4.759%) in intersection # overall time for all swap # real 294m29.066s ############################################################################## # LASTZ Chinese hamster CHO GCF_003668045.3 (DONE - 2020-12-08 - Hiram) mkdir /hive/data/genomes/mm39/bed/lastzGCF_003668045.3.2020-12-08 cd /hive/data/genomes/mm39/bed/lastzGCF_003668045.3.2020-12-08 printf '# GCF_003668045.3 vs mm39 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: Mouse Mm39 SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes SEQ1_CHUNK=20000000 SEQ1_LAP=10000 # QUERY: Chinese hamster GCF_003668045.3 SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/003/668/045/GCF_003668045.3/GCF_003668045.3.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/003/668/045/GCF_003668045.3/GCF_003668045.3.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm39/bed/lastzGCF_003668045.3.2020-12-08 TMPDIR=/dev/shm ' > DEF export targetDb="mm39" export asmId="GCF_003668045.3" export accessionId="${asmId}_CriGri-PICRH-1.0" export gcPath="GCF/003/668/045" cd /hive/data/genomes/${targetDb}/bed/lastz${asmId}.2020-12-08 time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 291m46.571s sed -e 's/^/ # /;' fb.$targetDb.chain.${asmId}Link.txt # 1582370207 bases of 2728222451 (58.000%) in intersection sed -e 's/^/ # /;' fb.$targetDb.chainSyn.${asmId}Link.txt # 1484311234 bases of 2728222451 (54.406%) in intersection time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2Bit="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.2bit" \ -querySizes="/hive/data/genomes/asmHubs/$gcPath/${asmId}/${asmId}.chrom.sizes.txt" \ $targetDb ${asmId}) >> rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 821m47.400s sed -e 's/^/ # /;' fb.$targetDb.chainRBest.$asmId.txt # 1455588785 bases of 2728222451 (53.353%) in intersection ### XXX haven't done this yet export target="mm39" export Target="Mm39" export query="GCF_003668045.3" export asmId="GCF_003668045.3_CriGri-PICRH-1.0" export gcPath="GCF/003/668/045" mkdir /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap cd /hive/data/genomes/asmHubs/refseqBuild/$gcPath/$asmId/trackData/blastz.$target.swap time (doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 -swapDir=`pwd` \ /hive/data/genomes/${target}/bed/lastz.${query}/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -swap -chainMinScore=3000 -chainLinearGap=medium) >> swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 70m57.610s missed this measurement sed -e 's/^/ # /;' fb.${query}.chain.${Target}Link.txt # 1557925479 bases of 2366634374 (65.829%) in intersection sed -e 's/^/ # /;' fb.${query}.chainSyn.${Target}Link.txt # 1455333889 bases of 2366634374 (61.494%) in intersection time (doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/$gcPath/${query}/${query}.chrom.sizes.txt" \ $query $target) >> rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 798m57.398s sed -e 's/^/ # /;' fb.${query}.chainRBest.${Target}.txt # 1456469555 bases of 2366634374 (61.542%) in intersection ############################################################################## # LASTZ X. tropicalis xenTro10 (DONE - 2021-02-22 - Hiram) mkdir /hive/data/genomes/mm39/bed/lastzXenTro10.2021-02-22 cd /hive/data/genomes/mm39/bed/lastzXenTro10.2021-02-22 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 XenTro10 SEQ2_DIR=/hive/data/genomes/xenTro10/xenTro10.2bit SEQ2_LEN=/hive/data/genomes/xenTro10/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm39/bed/lastzXenTro10.2021-02-22 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 231m18.929s sed -e 's/^/ # /;' fb.mm39.chainXenTro10Link.txt # 53459877 bases of 2654624157 (2.014%) in intersection sed -e 's/^/ # /;' fb.mm39.chainSynXenTro10Link.txt # 22503702 bases of 2654624157 (0.848%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ mm39 xenTro10) > rbest.log 2>&1 # real 188m44.842s sed -e's/^/ # /;' fb.mm39.chainRBest.XenTro10.txt # 38090013 bases of 2654624157 (1.435%) in intersection mkdir /hive/data/genomes/xenTro10/bed/blastz.mm39.swap cd /hive/data/genomes/xenTro10/bed/blastz.mm39.swap time (doBlastzChainNet.pl -noDbNameCheck -swap -verbose=2 \ /hive/data/genomes/mm39/bed/lastzXenTro10.2021-02-22/DEF \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 # real 11m51.841s sed -e 's/^/ # /;' fb.xenTro10.chainMm39Link.txt # 69880088 bases of 1448461978 (4.824%) in intersection sed -e 's/^/ # /;' fb.xenTro10.chainSynMm39Link.txt # 22992776 bases of 1448461978 (1.587%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ xenTro10 mm39) > rbest.log 2>&1 # real 189m59.538s sed -e 's/^/ # /;' fb.xenTro10.chainRBest.Mm39.txt # 37509757 bases of 1448461978 (2.590%) in intersection ############################################################################## # LASTZ boxer Tasha canFam6 (DONE - 2021-05-18 - Hiram) # establish a screen to control this job mkdir /hive/data/genomes/mm39/bed/lastzCanFam6.2021-05-18 cd /hive/data/genomes/mm39/bed/lastzCanFam6.2021-05-18 printf '# boxer Tasha canFam6 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: boxer Tasha canFam6 SEQ2_DIR=/hive/data/genomes/canFam6/canFam6.2bit SEQ2_LEN=/hive/data/genomes/canFam6/chrom.sizes SEQ2_CHUNK=10000000 SEQ2_LIMIT=20 SEQ2_LAP=0 BASE=/hive/data/genomes/mm39/bed/lastzCanFam6.2021-05-18 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 218m56.391s sed -e 's/^/ # /;' fb.mm39.chainCanFam6Link.txt # 769381640 bases of 2654624157 (28.983%) in intersection sed -e 's/^/ # /;' fb.mm39.chainSynCanFam6Link.txt # 727357801 bases of 2654624157 (27.400%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev mm39 canFam6 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 227m46.230s sed -e 's/^/ # /;' fb.mm39.chainRBest.CanFam6.txt # 732010764 bases of 2654624157 (27.575%) in intersection mkdir /hive/data/genomes/canFam6/bed/blastz.mm39.swap cd /hive/data/genomes/canFam6/bed/blastz.mm39.swap time (doBlastzChainNet.pl -verbose=2 \ /hive/data/genomes/mm39/bed/lastzCanFam6.2021-05-18/DEF \ -swap -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 & # real 45m15.626s sed -e 's/^/ # /;' fb.canFam6.chainMm39Link.txt # 749339105 bases of 2312743346 (32.400%) in intersection sed -e 's/^/ # /;' fb.canFam6.chainSynMm39Link.txt # 721148735 bases of 2312743346 (31.182%) in intersection time (doRecipBest.pl -load -workhorse=hgwdev canFam6 mm39 \ -buildDir=`pwd` -workhorse=hgwdev) > rbest.log 2>&1 & # real 204m49.212s sed -e 's/^/ # /;' fb.canFam6.chainRBest.Mm39.txt # 730973192 bases of 2312743346 (31.606%) in intersection ############################################################################## # LASTZ human hg19 (DONE - 2021-09-30 - Hiram) # should be able to run this from anywhere, this time it was run from: cd /hive/data/genomes/mm39/bed time (~/kent/src/hg/utils/automation/pairLastz.sh mm39 hg19 mammal primate) \ > mm39.hg19.log 2>&1 grep -w real mm39.hg19.log | tail -1 | sed -e 's/^/ # /;' # real 1200m57.924s # this command outputs this makeDoc text: cat lastz.hg19/makeDoc.txt ############################################################################## # LASTZ Mouse Mm39 vs. Human Hg19 (DONE - 2021-09-30 - Hiram) mkdir /hive/data/genomes/mm39/bed/lastzHg19.2021-09-30 cd /hive/data/genomes/mm39/bed/lastzHg19.2021-09-30 printf '# Human Hg19 vs. Mouse Mm39 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 SEQ1_LIMIT=40 # QUERY: Human Hg19 SEQ2_DIR=/hive/data/genomes/hg19/hg19.2bit SEQ2_LEN=/hive/data/genomes/hg19/chrom.sizes SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm39/bed/lastzHg19.2021-09-30 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -verbose=2 `pwd`/DEF -syntenicNet \ -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 474m8.118s # # real 474m8.118s # # real 370m29.622s # real 844m37.788s sed -e 's/^/ # /;' fb.mm39.chainHg19Link.txt # 938444606 bases of 2654624157 (35.351%) in intersection ### and for the swap cd /hive/data/genomes/hg19/bed/blastz.mm39.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ /hive/data/genomes/mm39/bed/lastzHg19.2021-09-30/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 57m17.328s sed -e 's/^/ # /;' fb.hg19.chainMm39Link.txt # 969322683 bases of 2991710746 (32.400%) in intersection sed -e 's/^/ # /;' fb.hg19.chainSynMm39Link.txt # 921405754 bases of 2991710746 (30.799%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ hg19 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 299m2.449s sed -e 's/^/ # /;' fb.hg19.chainRBest.Mm39.txt # 892863094 bases of 2991710746 (29.845%) in intersection ############################################################################## # LASTZ Mouse Mm39 vs. Seba's short-tailed bat GCA_004027735.1 (DONE - 2022-10-10 - Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation time (~/kent/src/hg/utils/automation/pairLastz.sh \ mm39 GCA_004027735.1_CarPer_v1_BIUU mammal mammal) \ > mm39.GCA_004027735.1_20221010.log 2>&1 & # check the total time grep -w real mm39.GCA_004027735.1_20221010.log | tail -1 | sed -e 's/^/ # /;' # real 4941m5.588s # this command outputs this makeDoc text: cat /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10/makeDoc.txt ############################################################################## # LASTZ Mouse Mm39 vs. Seba's short-tailed bat GCA_004027735.1 # (DONE - 2022-10-10 - Gerardo) mkdir /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10 cd /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10 printf '# Seba's short-tailed bat GCA_004027735.1 vs. Mouse Mm39 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 SEQ1_LIMIT=40 # QUERY: Seba's short-tailed bat 2019-01-16 GCA_004027735.1_CarPer_v1_BIUU SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=500 BASE=/hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_004027735.1_CarPer_v1_BIUU -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 682m7.456s sed -e 's/^/ # /;' fb.mm39.chainGCA_004027735.1Link.txt # 646007750 bases of 2728222451 (23.679%) in intersection sed -e 's/^/ # /;' fb.mm39.chainSynGCA_004027735.1Link.txt # 266104069 bases of 2728222451 (9.754%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.chrom.sizes.txt" \ mm39 GCA_004027735.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 514m58.090s sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_004027735.1.txt # 613273332 bases of 2728222451 (22.479%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/004/027/735/GCA_004027735.1_CarPer_v1_BIUU/trackData/blastz.mm39.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_004027735.1_CarPer_v1_BIUU /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 1925m11.716s sed -e 's/^/ # /;' fb.GCA_004027735.1.chainMm39Link.txt # 687442098 bases of 2689411905 (25.561%) in intersection sed -e 's/^/ # /;' fb.GCA_004027735.1.chainSynMm39Link.txt # 261303649 bases of 2689411905 (9.716%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.chrom.sizes.txt" \ GCA_004027735.1 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 1818m46.969s sed -e 's/^/ # /;' fb.GCA_004027735.1.chainRBest.Mm39.txt # 614276787 bases of 2689411905 (22.841%) in intersection ############################################################################## # Mm39 vs. eastern European house mouse GCA_001624775.1 (DONE - 2022-10-29 - Gerardo) time (~/kent/src/hg/utils/automation/pairLastz.sh \ mm39 GCA_001624775.1_PWK_PhJ_v1 mammal mammal) \ > mm39.GCA_001624775.1_20221029.log 2>&1 & # check the total time grep -w real mm39.GCA_001624775.1_20221029.log | tail -1 | sed -e 's/^/ # /;' # real 1337m18.429s # this command outputs this makeDoc text: cat /hive/data/genomes/mm39/bed/lastzGCA_001624775.1.2022-10-29/makeDoc.txt ############################################################################## # LASTZ Mouse Mm39 vs. eastern European house mouse GCA_001624775.1 # (DONE - 2022-10-29 - Gerardo) mkdir /hive/data/genomes/mm39/bed/lastzGCA_001624775.1.2022-10-29 cd /hive/data/genomes/mm39/bed/lastzGCA_001624775.1.2022-10-29 printf '# eastern European house mouse GCA_001624775.1 vs. Mouse Mm39 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 SEQ1_LIMIT=40 # QUERY: eastern European house mouse 2016-04-26 GCA_001624775.1_PWK_PhJ_v1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm39/bed/lastzGCA_001624775.1.2022-10-29 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_001624775.1_PWK_PhJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 796m20.050s sed -e 's/^/ # /;' fb.mm39.chainGCA_001624775.1Link.txt # 2352701230 bases of 2728222451 (86.236%) in intersection sed -e 's/^/ # /;' fb.mm39.chainSynGCA_001624775.1Link.txt # 2250688932 bases of 2728222451 (82.497%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.chrom.sizes.txt" \ mm39 GCA_001624775.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 140m24.553s sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_001624775.1.txt # 2217435105 bases of 2728222451 (81.278%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/001/624/775/GCA_001624775.1_PWK_PhJ_v1/trackData/blastz.mm39.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_001624775.1_PWK_PhJ_v1 /hive/data/genomes/mm39/bed/lastzGCA_001624775.1.2022-10-29/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 272m39.311s sed -e 's/^/ # /;' fb.GCA_001624775.1.chainMm39Link.txt # 2243083403 bases of 2559987392 (87.621%) in intersection sed -e 's/^/ # /;' fb.GCA_001624775.1.chainSynMm39Link.txt # 2222161260 bases of 2559987392 (86.804%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/775/GCA_001624775.1/GCA_001624775.1.chrom.sizes.txt" \ GCA_001624775.1 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 127m54.093s sed -e 's/^/ # /;' fb.GCA_001624775.1.chainRBest.Mm39.txt # 2221859352 bases of 2559987392 (86.792%) in intersection ############################################################################## # LASTZ Mouse Mm39 vs. western European house mouse GCA_001624835.1 (DONE - 2022-10-29 - Gerardo) time (~/kent/src/hg/utils/automation/pairLastz.sh \ mm39 GCA_001624835.1_WSB_EiJ_v1 mammal mammal) \ > mm39.GCA_001624835.1_20221029.log 2>&1 & # check the total time grep -w real mm39.GCA_001624835.1_20221029.log | tail -1 | sed -e 's/^/ # /;' # real 1435m16.301s # this command outputs this makeDoc text: cat /hive/data/genomes/mm39/bed/lastzGCA_001624835.1.2022-10-29/makeDoc.txt ############################################################################## # LASTZ Mouse Mm39 vs. western European house mouse GCA_001624835.1 # (DONE - 2022-10-29 - Gerardo) mkdir /hive/data/genomes/mm39/bed/lastzGCA_001624835.1.2022-10-29 cd /hive/data/genomes/mm39/bed/lastzGCA_001624835.1.2022-10-29 printf '# western European house mouse GCA_001624835.1 vs. Mouse Mm39 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 SEQ1_LIMIT=40 # QUERY: western European house mouse 2016-04-26 GCA_001624835.1_WSB_EiJ_v1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/mm39/bed/lastzGCA_001624835.1.2022-10-29 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -qAsmId GCA_001624835.1_WSB_EiJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 1043m35.512s sed -e 's/^/ # /;' fb.mm39.chainGCA_001624835.1Link.txt # 2340951592 bases of 2728222451 (85.805%) in intersection sed -e 's/^/ # /;' fb.mm39.chainSynGCA_001624835.1Link.txt # 2248126645 bases of 2728222451 (82.403%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -query2Bit="/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.chrom.sizes.txt" \ mm39 GCA_001624835.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 83m41.863s sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_001624835.1.txt # 2216500165 bases of 2728222451 (81.243%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/001/624/835/GCA_001624835.1_WSB_EiJ_v1/trackData/blastz.mm39.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -qAsmId GCA_001624835.1_WSB_EiJ_v1 /hive/data/genomes/mm39/bed/lastzGCA_001624835.1.2022-10-29/DEF -swapDir=`pwd` \ -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' # real 245m21.222s sed -e 's/^/ # /;' fb.GCA_001624835.1.chainMm39Link.txt # 2231272516 bases of 2689657557 (82.957%) in intersection sed -e 's/^/ # /;' fb.GCA_001624835.1.chainSynMm39Link.txt # 2222181450 bases of 2689657557 (82.619%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/835/GCA_001624835.1/GCA_001624835.1.chrom.sizes.txt" \ GCA_001624835.1 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 62m37.202s sed -e 's/^/ # /;' fb.GCA_001624835.1.chainRBest.Mm39.txt # 2218790179 bases of 2689657557 (82.493%) in intersection +############################################################################## +# LASTZ Mouse Mm39 vs. southeastern Asian house mouse GCA_001624445.1 +# (DONE - 2023-04-07 - Gerardo) + + mkdir /hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07 + cd /hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07 + + printf '# southeastern Asian house mouse GCA_001624445.1 vs. Mouse Mm39 +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 +SEQ1_LIMIT=40 + +# QUERY: southeastern Asian house mouse 2016-04-26 GCA_001624445.1_CAST_EiJ_v1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_001624445.1_CAST_EiJ_v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1058m44.662s + sed -e 's/^/ # /;' fb.mm39.chainGCA_001624445.1Link.txt + # 2329782432 bases of 2728222451 (85.396%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCA_001624445.1Link.txt + # 2229270653 bases of 2728222451 (81.711%) in intersection + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.chrom.sizes.txt" \ + mm39 GCA_001624445.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 127m51.046s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_001624445.1.txt + # 2199319876 bases of 2728222451 (80.614%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/001/624/445/GCA_001624445.1_CAST_EiJ_v1/trackData/blastz.mm39.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_001624445.1_CAST_EiJ_v1 /hive/data/genomes/mm39/bed/lastzGCA_001624445.1.2023-04-07/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 106m53.512s + + sed -e 's/^/ # /;' fb.GCA_001624445.1.chainMm39Link.txt + # 2223373125 bases of 2653990650 (83.775%) in intersection + sed -e 's/^/ # /;' fb.GCA_001624445.1.chainSynMm39Link.txt + # 2205392126 bases of 2653990650 (83.097%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/001/624/445/GCA_001624445.1/GCA_001624445.1.chrom.sizes.txt" \ + GCA_001624445.1 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 99m38.174s + + sed -e 's/^/ # /;' fb.GCA_001624445.1.chainRBest.Mm39.txt + # 2202774272 bases of 2653990650 (82.999%) in intersection + +real 1393m12.216s +user 0m2.744s +sys 0m1.859s +##############################################################################