06620dfabbaddbf072cc7da2ed8085377a1b173b gperez2 Tue Jun 17 18:43:50 2025 -0700 domestic yak (GCA_005887515.3) to sheep(GCF_016772045.2)/goat(GCF_001704415.2) lastz/chain/net run for user, refs #35876 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index ec23d890bd2..4c598c9d743 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -4389,15 +4389,184 @@ -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 ############################################################################## +# LASTZ domestic yak GCA_005887515.3 vs. goat GCF_001704415.2 +# (DONE - 2025-06-13 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/005/887/515/GCA_005887515.3_BosGru3.1/trackData/lastzGCF_001704415.2.2025-06-13 + cd /hive/data/genomes/asmHubs/allBuild/GCA/005/887/515/GCA_005887515.3_BosGru3.1/trackData/lastzGCF_001704415.2.2025-06-13 + + printf '# goat GCF_001704415.2 vs. domestic yak GCA_005887515.3 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: domestic yak 2019-06-10 GCA_005887515.3_BosGru3.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: goat 2016-08-24 GCF_001704415.2_ARS1.2 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCA/005/887/515/GCA_005887515.3_BosGru3.1/trackData/lastzGCF_001704415.2.2025-06-13 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_005887515.3_BosGru3.1 -qAsmId GCF_001704415.2_ARS1.2 -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 826m9.350s + + sed -e 's/^/ # /;' fb.GCA_005887515.3.chainGCF_001704415.2Link.txt + # 2554401007 bases of 2831460571 (90.215%) in intersection + sed -e 's/^/ # /;' fb.GCA_005887515.3.chainSynGCF_001704415.2Link.txt + # 2424392229 bases of 2831460571 (85.623%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt" \ + GCA_005887515.3 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 940m58.790s + + sed -e 's/^/ # /;' fb.GCA_005887515.3.chainRBest.GCF_001704415.2.txt + # 2238316806 bases of 2831460571 (79.052%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCA_005887515.3.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCA_005887515.3_BosGru3.1 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCA/005/887/515/GCA_005887515.3_BosGru3.1/trackData/lastzGCF_001704415.2.2025-06-13/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 210m33.382s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCA_005887515.3Link.txt + # 2385596646 bases of 2922617086 (81.625%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCA_005887515.3Link.txt + # 2262243284 bases of 2922617086 (77.405%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt" \ + GCF_001704415.2 GCA_005887515.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 414m0.992s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCA_005887515.3.txt + # 2236235583 bases of 2922617086 (76.515%) in intersection + +real 2391m52.326s +user 0m5.147s +sys 0m3.126s +############################################################################## +# LASTZ domestic yak GCA_005887515.3 vs. sheep GCF_016772045.2 +# (DONE - 2025-06-13 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/005/887/515/GCA_005887515.3_BosGru3.1/trackData/lastzGCF_016772045.2.2025-06-13 + cd /hive/data/genomes/asmHubs/allBuild/GCA/005/887/515/GCA_005887515.3_BosGru3.1/trackData/lastzGCF_016772045.2.2025-06-13 + + printf '# sheep GCF_016772045.2 vs. domestic yak GCA_005887515.3 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: domestic yak 2019-06-10 GCA_005887515.3_BosGru3.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: sheep 2023-07-20 GCF_016772045.2_ARS-UI_Ramb_v3.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCA/005/887/515/GCA_005887515.3_BosGru3.1/trackData/lastzGCF_016772045.2.2025-06-13 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_005887515.3_BosGru3.1 -qAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0 -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 657m12.826s + + sed -e 's/^/ # /;' fb.GCA_005887515.3.chainGCF_016772045.2Link.txt + # 2552012126 bases of 2831460571 (90.131%) in intersection + sed -e 's/^/ # /;' fb.GCA_005887515.3.chainSynGCF_016772045.2Link.txt + # 2428650508 bases of 2831460571 (85.774%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \ + GCA_005887515.3 GCF_016772045.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 1310m5.661s + + sed -e 's/^/ # /;' fb.GCA_005887515.3.chainRBest.GCF_016772045.2.txt + # 2237425562 bases of 2831460571 (79.020%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/772/045/GCF_016772045.2_ARS-UI_Ramb_v3.0/trackData/blastz.GCA_005887515.3.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCA_005887515.3_BosGru3.1 -qAsmId GCF_016772045.2_ARS-UI_Ramb_v3.0 /hive/data/genomes/asmHubs/allBuild/GCA/005/887/515/GCA_005887515.3_BosGru3.1/trackData/lastzGCF_016772045.2.2025-06-13/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 219m56.040s + + sed -e 's/^/ # /;' fb.GCF_016772045.2.chainGCA_005887515.3Link.txt + # 2357377167 bases of 2654063983 (88.821%) in intersection + sed -e 's/^/ # /;' fb.GCF_016772045.2.chainSynGCA_005887515.3Link.txt + # 2239198320 bases of 2654063983 (84.369%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/005/887/515/GCA_005887515.3/GCA_005887515.3.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.2/GCF_016772045.2.chrom.sizes.txt" \ + GCF_016772045.2 GCA_005887515.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 427m9.377s + + sed -e 's/^/ # /;' fb.GCF_016772045.2.chainRBest.GCA_005887515.3.txt + # 2234989367 bases of 2654063983 (84.210%) in intersection + +real 2614m35.639s +user 0m4.451s +sys 0m3.505s