60926b22b0e71a92f99d8ed72f494a0689f06fa4 gperez2 Sat Jun 14 12:20:50 2025 -0700 cattle (GCF_002263795.3) to wildyak/pig/horse/dog/sugar_glider/rabbit/hedgehog lastz/chain/net run for user, refs #35794 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index fb1d408b3b9..ec23d890bd2 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -3793,15 +3793,611 @@ # 1457737528 bases of 2501912388 (58.265%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCF/000/003/025/GCF_000003025.6/GCF_000003025.6.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/003/025/GCF_000003025.6/GCF_000003025.6.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ GCF_000003025.6 GCF_002263795.3) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 273m18.460s real 2275m33.144s user 0m3.060s sys 0m3.413s +############################################################################## +# LASTZ domestic cattle GCF_002263795.3 vs. dog GCF_011100685.1 +# (DONE - 2025-05-24 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_011100685.1.2025-05-24 + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_011100685.1.2025-05-24 + + printf '# dog GCF_011100685.1 vs. domestic cattle GCF_002263795.3 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: dog 2020-03-10 GCF_011100685.1_UU_Cfam_GSD_1.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_011100685.1.2025-05-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_002263795.3_ARS-UCD2.0 -qAsmId GCF_011100685.1_UU_Cfam_GSD_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 684m22.996s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainGCF_011100685.1Link.txt + # 1423951424 bases of 2770686120 (51.393%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynGCF_011100685.1Link.txt + # 1379510588 bases of 2770686120 (49.789%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.chrom.sizes.txt" \ + GCF_002263795.3 GCF_011100685.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 142m53.958s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.GCF_011100685.1.txt + # 1358221321 bases of 2770686120 (49.021%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/011/100/685/GCF_011100685.1_UU_Cfam_GSD_1.0/trackData/blastz.GCF_002263795.3.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_002263795.3_ARS-UCD2.0 -qAsmId GCF_011100685.1_UU_Cfam_GSD_1.0 /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_011100685.1.2025-05-24/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 64m31.734s + + sed -e 's/^/ # /;' fb.GCF_011100685.1.chainGCF_002263795.3Link.txt + # 1426629471 bases of 2481983352 (57.479%) in intersection + sed -e 's/^/ # /;' fb.GCF_011100685.1.chainSynGCF_002263795.3Link.txt + # 1377068775 bases of 2481983352 (55.483%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/011/100/685/GCF_011100685.1/GCF_011100685.1.chrom.sizes.txt" \ + GCF_011100685.1 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 142m0.161s + + sed -e 's/^/ # /;' fb.GCF_011100685.1.chainRBest.GCF_002263795.3.txt + # 1357354893 bases of 2481983352 (54.688%) in intersection + +real 1033m59.572s +user 0m3.625s +sys 0m3.623s + +############################################################################## +# LASTZ domestic cattle GCF_002263795.3 vs. Horse EquCab3 +# (DONE - 2025-05-24 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzEquCab3.2025-05-24 + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzEquCab3.2025-05-24 + + printf '# Horse EquCab3 vs. domestic cattle GCF_002263795.3 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# 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/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzEquCab3.2025-05-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_002263795.3_ARS-UCD2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 669m33.128s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainEquCab3Link.txt + # 1566422550 bases of 2770686120 (56.536%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynEquCab3Link.txt + # 1501111481 bases of 2770686120 (54.178%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + \ + GCF_002263795.3 equCab3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 184m22.383s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.EquCab3.txt + # 1479409010 bases of 2770686120 (53.395%) in intersection + + ### and for the swap + + cd /hive/data/genomes/equCab3/bed/blastz.GCF_002263795.3.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_002263795.3_ARS-UCD2.0 /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzEquCab3.2025-05-24/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 79m41.596s + + sed -e 's/^/ # /;' fb.equCab3.chainGCF_002263795.3Link.txt + # 1588835758 bases of 2506966135 (63.377%) in intersection + sed -e 's/^/ # /;' fb.equCab3.chainSynGCF_002263795.3Link.txt + # 1531394047 bases of 2506966135 (61.086%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + \ + equCab3 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 148m48.055s + + sed -e 's/^/ # /;' fb.equCab3.chainRBest.GCF_002263795.3.txt + # 1477925035 bases of 2506966135 (58.953%) in intersection + +real 1082m32.448s +user 0m2.679s +sys 0m2.475s +############################################################################## +# LASTZ domestic cattle GCF_002263795.3 vs. wild yak GCF_027580195.1 +# (DONE - 2025-05-24 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_027580195.1.2025-05-24 + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_027580195.1.2025-05-24 + + printf '# wild yak GCF_027580195.1 vs. domestic cattle GCF_002263795.3 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: wild yak 2023-01-09 GCF_027580195.1_NWIPB_WYAK_1.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/027/580/195/GCF_027580195.1/GCF_027580195.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/027/580/195/GCF_027580195.1/GCF_027580195.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_027580195.1.2025-05-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_002263795.3_ARS-UCD2.0 -qAsmId GCF_027580195.1_NWIPB_WYAK_1.1 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 807m11.402s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainGCF_027580195.1Link.txt + # 2649773337 bases of 2770686120 (95.636%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynGCF_027580195.1Link.txt + # 2622051809 bases of 2770686120 (94.635%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/027/580/195/GCF_027580195.1/GCF_027580195.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/027/580/195/GCF_027580195.1/GCF_027580195.1.chrom.sizes.txt" \ + GCF_002263795.3 GCF_027580195.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 63m31.690s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.GCF_027580195.1.txt + # 2560941301 bases of 2770686120 (92.430%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/027/580/195/GCF_027580195.1_NWIPB_WYAK_1.1/trackData/blastz.GCF_002263795.3.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_002263795.3_ARS-UCD2.0 -qAsmId GCF_027580195.1_NWIPB_WYAK_1.1 /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_027580195.1.2025-05-24/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 171m28.116s + + sed -e 's/^/ # /;' fb.GCF_027580195.1.chainGCF_002263795.3Link.txt + # 2599654471 bases of 2626917182 (98.962%) in intersection + sed -e 's/^/ # /;' fb.GCF_027580195.1.chainSynGCF_002263795.3Link.txt + # 2578063356 bases of 2626917182 (98.140%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/027/580/195/GCF_027580195.1/GCF_027580195.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/027/580/195/GCF_027580195.1/GCF_027580195.1.chrom.sizes.txt" \ + GCF_027580195.1 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 64m59.432s + + sed -e 's/^/ # /;' fb.GCF_027580195.1.chainRBest.GCF_002263795.3.txt + # 2561422780 bases of 2626917182 (97.507%) in intersection + +real 1107m20.747s +user 0m3.579s +sys 0m3.133s + +############################################################################## +# LASTZ sugar glider GCF_028583685.1 vs. domestic cattle GCF_002263795.3 +# (DONE - 2025-05-24 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/028/583/685/GCF_028583685.1_PetGlider_PUasm1.0/trackData/lastzGCF_002263795.3.2025-05-24 + cd /hive/data/genomes/asmHubs/allBuild/GCF/028/583/685/GCF_028583685.1_PetGlider_PUasm1.0/trackData/lastzGCF_002263795.3.2025-05-24 + + printf '# domestic cattle GCF_002263795.3 vs. sugar glider GCF_028583685.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: sugar glider 2023-02-10 GCF_028583685.1_PetGlider_PUasm1.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/028/583/685/GCF_028583685.1/GCF_028583685.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/028/583/685/GCF_028583685.1/GCF_028583685.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/028/583/685/GCF_028583685.1_PetGlider_PUasm1.0/trackData/lastzGCF_002263795.3.2025-05-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_028583685.1_PetGlider_PUasm1.0 -qAsmId GCF_002263795.3_ARS-UCD2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 597m54.509s + + sed -e 's/^/ # /;' fb.GCF_028583685.1.chainGCF_002263795.3Link.txt + # 255707425 bases of 3464720375 (7.380%) in intersection + sed -e 's/^/ # /;' fb.GCF_028583685.1.chainSynGCF_002263795.3Link.txt + # 80726755 bases of 3464720375 (2.330%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/028/583/685/GCF_028583685.1/GCF_028583685.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/028/583/685/GCF_028583685.1/GCF_028583685.1.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + GCF_028583685.1 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 312m23.029s + + sed -e 's/^/ # /;' fb.GCF_028583685.1.chainRBest.GCF_002263795.3.txt + # 192515429 bases of 3464720375 (5.556%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/blastz.GCF_028583685.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_028583685.1_PetGlider_PUasm1.0 -qAsmId GCF_002263795.3_ARS-UCD2.0 /hive/data/genomes/asmHubs/allBuild/GCF/028/583/685/GCF_028583685.1_PetGlider_PUasm1.0/trackData/lastzGCF_002263795.3.2025-05-24/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 14m43.296s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainGCF_028583685.1Link.txt + # 227332898 bases of 2770686120 (8.205%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynGCF_028583685.1Link.txt + # 78758585 bases of 2770686120 (2.843%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/028/583/685/GCF_028583685.1/GCF_028583685.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/028/583/685/GCF_028583685.1/GCF_028583685.1.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + GCF_002263795.3 GCF_028583685.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 290m58.089s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.GCF_028583685.1.txt + # 193370884 bases of 2770686120 (6.979%) in intersection + +real 1216m9.656s +user 0m3.034s +sys 0m3.531s + +############################################################################## +# LASTZ Pig SusScr11 vs. domestic cattle GCF_002263795.3 +# (DONE - 2025-05-24 - Gerardo) + + mkdir /hive/data/genomes/susScr11/bed/lastzGCF_002263795.3.2025-05-24 + cd /hive/data/genomes/susScr11/bed/lastzGCF_002263795.3.2025-05-24 + + printf '# domestic cattle GCF_002263795.3 vs. Pig SusScr11 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Pig susScr11 +SEQ1_DIR=/hive/data/genomes/susScr11/susScr11.2bit +SEQ1_LEN=/hive/data/genomes/susScr11/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/susScr11/bed/lastzGCF_002263795.3.2025-05-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_002263795.3_ARS-UCD2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 660m46.932s + + sed -e 's/^/ # /;' fb.susScr11.chainGCF_002263795.3Link.txt + # 1538671069 bases of 2501912388 (61.500%) in intersection + sed -e 's/^/ # /;' fb.susScr11.chainSynGCF_002263795.3Link.txt + # 1458472814 bases of 2501912388 (58.294%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + susScr11 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 326m9.575s + + sed -e 's/^/ # /;' fb.susScr11.chainRBest.GCF_002263795.3.txt + # 1451216570 bases of 2501912388 (58.004%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/blastz.susScr11.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_002263795.3_ARS-UCD2.0 /hive/data/genomes/susScr11/bed/lastzGCF_002263795.3.2025-05-24/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 87m34.401s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSusScr11Link.txt + # 1564330808 bases of 2770686120 (56.460%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynSusScr11Link.txt + # 1468392204 bases of 2770686120 (52.997%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + GCF_002263795.3 susScr11) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 286m26.237s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.SusScr11.txt + # 1452487324 bases of 2770686120 (52.423%) in intersection + +real 1361m5.862s +user 0m2.697s +sys 0m3.106s + +############################################################################## +# LASTZ western European hedgehog GCF_950295315.1 vs. domestic cattle GCF_002263795.3 +# (DONE - 2025-05-24 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/950/295/315/GCF_950295315.1_mEriEur2.1/trackData/lastzGCF_002263795.3.2025-05-24 + cd /hive/data/genomes/asmHubs/allBuild/GCF/950/295/315/GCF_950295315.1_mEriEur2.1/trackData/lastzGCF_002263795.3.2025-05-24 + + printf '# domestic cattle GCF_002263795.3 vs. western European hedgehog GCF_950295315.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: western European hedgehog 2023-05-01 GCF_950295315.1_mEriEur2.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/950/295/315/GCF_950295315.1_mEriEur2.1/trackData/lastzGCF_002263795.3.2025-05-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_950295315.1_mEriEur2.1 -qAsmId GCF_002263795.3_ARS-UCD2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 580m18.776s + + sed -e 's/^/ # /;' fb.GCF_950295315.1.chainGCF_002263795.3Link.txt + # 764669504 bases of 2720683831 (28.106%) in intersection + sed -e 's/^/ # /;' fb.GCF_950295315.1.chainSynGCF_002263795.3Link.txt + # 687796077 bases of 2720683831 (25.280%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + GCF_950295315.1 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 360m39.635s + + sed -e 's/^/ # /;' fb.GCF_950295315.1.chainRBest.GCF_002263795.3.txt + # 716090515 bases of 2720683831 (26.320%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/blastz.GCF_950295315.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_950295315.1_mEriEur2.1 -qAsmId GCF_002263795.3_ARS-UCD2.0 /hive/data/genomes/asmHubs/allBuild/GCF/950/295/315/GCF_950295315.1_mEriEur2.1/trackData/lastzGCF_002263795.3.2025-05-24/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 50m24.520s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainGCF_950295315.1Link.txt + # 845447519 bases of 2770686120 (30.514%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynGCF_950295315.1Link.txt + # 694290364 bases of 2770686120 (25.058%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/950/295/315/GCF_950295315.1/GCF_950295315.1.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + GCF_002263795.3 GCF_950295315.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 453m41.295s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.GCF_950295315.1.txt + # 712308468 bases of 2770686120 (25.709%) in intersection + +real 1445m15.885s +user 0m4.303s +sys 0m3.368s +############################################################################## +# LASTZ rabbit GCF_964237555.1 vs. domestic cattle GCF_002263795.3 +# (DONE - 2025-05-24 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/964/237/555/GCF_964237555.1_mOryCun1.1/trackData/lastzGCF_002263795.3.2025-05-24 + cd /hive/data/genomes/asmHubs/allBuild/GCF/964/237/555/GCF_964237555.1_mOryCun1.1/trackData/lastzGCF_002263795.3.2025-05-24 + + printf '# domestic cattle GCF_002263795.3 vs. rabbit GCF_964237555.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: rabbit 2024-08-31 GCF_964237555.1_mOryCun1.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/964/237/555/GCF_964237555.1/GCF_964237555.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/964/237/555/GCF_964237555.1/GCF_964237555.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/964/237/555/GCF_964237555.1_mOryCun1.1/trackData/lastzGCF_002263795.3.2025-05-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_964237555.1_mOryCun1.1 -qAsmId GCF_002263795.3_ARS-UCD2.0 -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 657m37.196s + + sed -e 's/^/ # /;' fb.GCF_964237555.1.chainGCF_002263795.3Link.txt + # 1222669510 bases of 2804657419 (43.594%) in intersection + sed -e 's/^/ # /;' fb.GCF_964237555.1.chainSynGCF_002263795.3Link.txt + # 1036327499 bases of 2804657419 (36.950%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/964/237/555/GCF_964237555.1/GCF_964237555.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/964/237/555/GCF_964237555.1/GCF_964237555.1.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + GCF_964237555.1 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 864m22.073s + + sed -e 's/^/ # /;' fb.GCF_964237555.1.chainRBest.GCF_002263795.3.txt + # 1061764998 bases of 2804657419 (37.857%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/blastz.GCF_964237555.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_964237555.1_mOryCun1.1 -qAsmId GCF_002263795.3_ARS-UCD2.0 /hive/data/genomes/asmHubs/allBuild/GCF/964/237/555/GCF_964237555.1_mOryCun1.1/trackData/lastzGCF_002263795.3.2025-05-24/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -fileServer=hgwdev -bigClusterHub=hgwdev \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 87m41.371s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainGCF_964237555.1Link.txt + # 1218100063 bases of 2770686120 (43.964%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynGCF_964237555.1Link.txt + # 1037474350 bases of 2770686120 (37.445%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/964/237/555/GCF_964237555.1/GCF_964237555.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/964/237/555/GCF_964237555.1/GCF_964237555.1.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + GCF_002263795.3 GCF_964237555.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 681m37.220s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.GCF_964237555.1.txt + # 1057024850 bases of 2770686120 (38.150%) in intersection + +real 2291m29.553s +user 0m3.803s +sys 0m3.589s +##############################################################################