7d1bd72b73f54dbacbb39445fbb6a1a3b0227433 jnavarr5 Tue Apr 21 13:55:18 2026 -0700 Adding liftOver runs for liftOver files a user requested, refs #37380 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index fbf5f5843f4..2fb71f8d70e 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -4799,15 +4799,1443 @@ sed -e 's/^/ # /;' fb.GCF_009873245.2.chainSynSusScr11Link.txt # 1596415268 bases of 2374868943 (67.221%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ \ -target2bit="/hive/data/genomes/asmHubs/GCF/009/873/245/GCF_009873245.2/GCF_009873245.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/009/873/245/GCF_009873245.2/GCF_009873245.2.chrom.sizes.txt" \ GCF_009873245.2 susScr11) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 333m23.268s sed -e 's/^/ # /;' fb.GCF_009873245.2.chainRBest.SusScr11.txt # 1613579672 bases of 2374868943 (67.944%) in intersection ############################################################################## + +############################################################################## +# LASTZ African savanna elephant GCA_000001905.1 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/000/001/905/GCA_000001905.1_Loxafr3.0/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCA/000/001/905/GCA_000001905.1_Loxafr3.0/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 vs. African savanna elephant GCA_000001905.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: African savanna elephant 2009-07-15 GCA_000001905.1_Loxafr3.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/000/001/905/GCA_000001905.1/GCA_000001905.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/000/001/905/GCA_000001905.1/GCA_000001905.1.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/000/001/905/GCA_000001905.1_Loxafr3.0/trackData/lastzGCF_001704415.2.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_000001905.1_Loxafr3.0 -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 755m11.159s + + sed -e 's/^/ # /;' fb.GCA_000001905.1.chainGCF_001704415.2Link.txt + # 1159915641 bases of 3196738035 (36.284%) in intersection + sed -e 's/^/ # /;' fb.GCA_000001905.1.chainSynGCF_001704415.2Link.txt + # 1109806856 bases of 3196738035 (34.717%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/000/001/905/GCA_000001905.1/GCA_000001905.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/000/001/905/GCA_000001905.1/GCA_000001905.1.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_000001905.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 170m51.046s + + sed -e 's/^/ # /;' fb.GCA_000001905.1.chainRBest.GCF_001704415.2.txt + # 1108965347 bases of 3196738035 (34.691%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCA_000001905.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCA_000001905.1_Loxafr3.0 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCA/000/001/905/GCA_000001905.1_Loxafr3.0/trackData/lastzGCF_001704415.2.2026-04-17/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 64m55.223s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCA_000001905.1Link.txt + # 1167717426 bases of 2922617086 (39.955%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCA_000001905.1Link.txt + # 1109055308 bases of 2922617086 (37.947%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCA/000/001/905/GCA_000001905.1/GCA_000001905.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/000/001/905/GCA_000001905.1/GCA_000001905.1.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_000001905.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 157m29.033s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCA_000001905.1.txt + # 1109593334 bases of 2922617086 (37.966%) in intersection + +############################################################################## + +############################################################################## +# LASTZ rabbit GCA_000003625.1 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/000/003/625/GCA_000003625.1_OryCun2.0/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCA/000/003/625/GCA_000003625.1_OryCun2.0/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 vs. rabbit GCA_000003625.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: rabbit 2009-10-20 GCA_000003625.1_OryCun2.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/000/003/625/GCA_000003625.1/GCA_000003625.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/000/003/625/GCA_000003625.1/GCA_000003625.1.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/000/003/625/GCA_000003625.1_OryCun2.0/trackData/lastzGCF_001704415.2.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_000003625.1_OryCun2.0 -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 782m51.200s + + sed -e 's/^/ # /;' fb.GCA_000003625.1.chainGCF_001704415.2Link.txt + # 1026389341 bases of 2737473256 (37.494%) in intersection + sed -e 's/^/ # /;' fb.GCA_000003625.1.chainSynGCF_001704415.2Link.txt + # 966786878 bases of 2737473256 (35.317%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/000/003/625/GCA_000003625.1/GCA_000003625.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/000/003/625/GCA_000003625.1/GCA_000003625.1.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_000003625.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 210m28.177s + + sed -e 's/^/ # /;' fb.GCA_000003625.1.chainRBest.GCF_001704415.2.txt + # 977011412 bases of 2737473256 (35.690%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCA_000003625.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCA_000003625.1_OryCun2.0 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCA/000/003/625/GCA_000003625.1_OryCun2.0/trackData/lastzGCF_001704415.2.2026-04-17/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 53m48.000s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCA_000003625.1Link.txt + # 1053163436 bases of 2922617086 (36.035%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCA_000003625.1Link.txt + # 968938772 bases of 2922617086 (33.153%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCA/000/003/625/GCA_000003625.1/GCA_000003625.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/000/003/625/GCA_000003625.1/GCA_000003625.1.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_000003625.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 206m14.967s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCA_000003625.1.txt + # 976293847 bases of 2922617086 (33.405%) in intersection + +############################################################################## + +############################################################################## +# LASTZ Blue whale GCA_009873245.2 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/009/873/245/GCA_009873245.2_mBalMus1.v2/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCA/009/873/245/GCA_009873245.2_mBalMus1.v2/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 vs. Blue whale GCA_009873245.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Blue whale 2020-02-03 GCA_009873245.2_mBalMus1.v2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/009/873/245/GCA_009873245.2/GCA_009873245.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/009/873/245/GCA_009873245.2/GCA_009873245.2.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/009/873/245/GCA_009873245.2_mBalMus1.v2/trackData/lastzGCF_001704415.2.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_009873245.2_mBalMus1.v2 -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 1409m15.264s + + sed -e 's/^/ # /;' fb.GCA_009873245.2.chainGCF_001704415.2Link.txt + # 1853615451 bases of 2380012384 (77.883%) in intersection + sed -e 's/^/ # /;' fb.GCA_009873245.2.chainSynGCF_001704415.2Link.txt + # 1592350587 bases of 2380012384 (66.905%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/009/873/245/GCA_009873245.2/GCA_009873245.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/009/873/245/GCA_009873245.2/GCA_009873245.2.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_009873245.2 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 270m13.968s + + sed -e 's/^/ # /;' fb.GCA_009873245.2.chainRBest.GCF_001704415.2.txt + # 1600089785 bases of 2380012384 (67.230%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCA_009873245.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCA_009873245.2_mBalMus1.v2 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCA/009/873/245/GCA_009873245.2_mBalMus1.v2/trackData/lastzGCF_001704415.2.2026-04-17/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 253m44.473s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCA_009873245.2Link.txt + # 1758738352 bases of 2922617086 (60.177%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCA_009873245.2Link.txt + # 1623133982 bases of 2922617086 (55.537%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCA/009/873/245/GCA_009873245.2/GCA_009873245.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/009/873/245/GCA_009873245.2/GCA_009873245.2.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_009873245.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 384m23.118s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCA_009873245.2.txt + # 1605999191 bases of 2922617086 (54.951%) in intersection + +############################################################################## + +############################################################################## +# LASTZ Norway rat GCA_036323735.1 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/036/323/735/GCA_036323735.1_GRCr8/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCA/036/323/735/GCA_036323735.1_GRCr8/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 vs. Norway rat GCA_036323735.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Norway rat 2024-01-31 GCA_036323735.1_GRCr8 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/036/323/735/GCA_036323735.1/GCA_036323735.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/036/323/735/GCA_036323735.1/GCA_036323735.1.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/036/323/735/GCA_036323735.1_GRCr8/trackData/lastzGCF_001704415.2.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_036323735.1_GRCr8 -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 790m44.525s + + sed -e 's/^/ # /;' fb.GCA_036323735.1.chainGCF_001704415.2Link.txt + # 720458043 bases of 2849597507 (25.283%) in intersection + sed -e 's/^/ # /;' fb.GCA_036323735.1.chainSynGCF_001704415.2Link.txt + # 645441677 bases of 2849597507 (22.650%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/036/323/735/GCA_036323735.1/GCA_036323735.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/036/323/735/GCA_036323735.1/GCA_036323735.1.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_036323735.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 262m40.418s + + sed -e 's/^/ # /;' fb.GCA_036323735.1.chainRBest.GCF_001704415.2.txt + # 662753884 bases of 2849597507 (23.258%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCA_036323735.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCA_036323735.1_GRCr8 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCA/036/323/735/GCA_036323735.1_GRCr8/trackData/lastzGCF_001704415.2.2026-04-17/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 39m53.535s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCA_036323735.1Link.txt + # 695356334 bases of 2922617086 (23.792%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCA_036323735.1Link.txt + # 644823288 bases of 2922617086 (22.063%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCA/036/323/735/GCA_036323735.1/GCA_036323735.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/036/323/735/GCA_036323735.1/GCA_036323735.1.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_036323735.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 241m47.457s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCA_036323735.1.txt + # 662188359 bases of 2922617086 (22.657%) in intersection + +############################################################################## + +############################################################################## +# LASTZ goat GCF_001704415.2 vs. domestic guinea pig GCA_000151735.1 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCA_000151735.1.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCA_000151735.1.2026-04-17 + + printf '# domestic guinea pig GCA_000151735.1 vs. goat GCF_001704415.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: goat 2016-08-24 GCF_001704415.2_ARS1.2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: domestic guinea pig 2008-03-03 GCA_000151735.1_Cavpor3.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/000/151/735/GCA_000151735.1/GCA_000151735.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/000/151/735/GCA_000151735.1/GCA_000151735.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCA_000151735.1.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCA_000151735.1_Cavpor3.0 -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 927m7.096s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCA_000151735.1Link.txt + # 983900574 bases of 2922617086 (33.665%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCA_000151735.1Link.txt + # 932870818 bases of 2922617086 (31.919%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/000/151/735/GCA_000151735.1/GCA_000151735.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/000/151/735/GCA_000151735.1/GCA_000151735.1.chrom.sizes.txt" \ + GCF_001704415.2 GCA_000151735.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 105m30.005s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCA_000151735.1.txt + # 941583973 bases of 2922617086 (32.217%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/000/151/735/GCA_000151735.1_Cavpor3.0/trackData/blastz.GCF_001704415.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCA_000151735.1_Cavpor3.0 /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCA_000151735.1.2026-04-17/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 60m59.037s + + sed -e 's/^/ # /;' fb.GCA_000151735.1.chainGCF_001704415.2Link.txt + # 1016845184 bases of 2723202840 (37.340%) in intersection + sed -e 's/^/ # /;' fb.GCA_000151735.1.chainSynGCF_001704415.2Link.txt + # 948446142 bases of 2723202840 (34.828%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -target2bit="/hive/data/genomes/asmHubs/GCA/000/151/735/GCA_000151735.1/GCA_000151735.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/000/151/735/GCA_000151735.1/GCA_000151735.1.chrom.sizes.txt" \ + GCA_000151735.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 131m28.605s + + sed -e 's/^/ # /;' fb.GCA_000151735.1.chainRBest.GCF_001704415.2.txt + # 943551205 bases of 2723202840 (34.649%) in intersection + +############################################################################## + +############################################################################## +# LASTZ goat GCF_001704415.2 vs. sika deer GCA_034195675.1 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCA_034195675.1.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCA_034195675.1.2026-04-17 + + printf '# sika deer GCA_034195675.1 vs. goat GCF_001704415.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: goat 2016-08-24 GCF_001704415.2_ARS1.2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: sika deer 2023-12-07 GCA_034195675.1_ASM3419567v1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/034/195/675/GCA_034195675.1/GCA_034195675.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/034/195/675/GCA_034195675.1/GCA_034195675.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCA_034195675.1.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCA_034195675.1_ASM3419567v1 -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 1037m40.744s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCA_034195675.1Link.txt + # 2370492694 bases of 2922617086 (81.109%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCA_034195675.1Link.txt + # 2242894846 bases of 2922617086 (76.743%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/034/195/675/GCA_034195675.1/GCA_034195675.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/034/195/675/GCA_034195675.1/GCA_034195675.1.chrom.sizes.txt" \ + GCF_001704415.2 GCA_034195675.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 359m8.284s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCA_034195675.1.txt + # 2221535054 bases of 2922617086 (76.012%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/034/195/675/GCA_034195675.1_ASM3419567v1/trackData/blastz.GCF_001704415.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCA_034195675.1_ASM3419567v1 /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCA_034195675.1.2026-04-17/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 149m58.764s + + sed -e 's/^/ # /;' fb.GCA_034195675.1.chainGCF_001704415.2Link.txt + # 2347008286 bases of 2541240779 (92.357%) in intersection + sed -e 's/^/ # /;' fb.GCA_034195675.1.chainSynGCF_001704415.2Link.txt + # 2231891668 bases of 2541240779 (87.827%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -target2bit="/hive/data/genomes/asmHubs/GCA/034/195/675/GCA_034195675.1/GCA_034195675.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/034/195/675/GCA_034195675.1/GCA_034195675.1.chrom.sizes.txt" \ + GCA_034195675.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 294m31.108s + + sed -e 's/^/ # /;' fb.GCA_034195675.1.chainRBest.GCF_001704415.2.txt + # 2219651564 bases of 2541240779 (87.345%) in intersection + +############################################################################## + +############################################################################## +# LASTZ goat GCF_001704415.2 vs. large flying fox GCF_000151845.1 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_000151845.1.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_000151845.1.2026-04-17 + + printf '# large flying fox GCF_000151845.1 vs. goat GCF_001704415.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: goat 2016-08-24 GCF_001704415.2_ARS1.2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: large flying fox 2014-12-05 GCF_000151845.1_Pvam_2.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/151/845/GCF_000151845.1/GCF_000151845.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/151/845/GCF_000151845.1/GCF_000151845.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_000151845.1.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCF_000151845.1_Pvam_2.0 -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 946m6.590s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_000151845.1Link.txt + # 1354233142 bases of 2922617086 (46.336%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_000151845.1Link.txt + # 1247823984 bases of 2922617086 (42.695%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/000/151/845/GCF_000151845.1/GCF_000151845.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/000/151/845/GCF_000151845.1/GCF_000151845.1.chrom.sizes.txt" \ + GCF_001704415.2 GCF_000151845.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 178m23.537s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_000151845.1.txt + # 1267457908 bases of 2922617086 (43.367%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/000/151/845/GCF_000151845.1_Pvam_2.0/trackData/blastz.GCF_001704415.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCF_000151845.1_Pvam_2.0 /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_000151845.1.2026-04-17/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 86m51.683s + + sed -e 's/^/ # /;' fb.GCF_000151845.1.chainGCF_001704415.2Link.txt + # 1373474935 bases of 2198284804 (62.479%) in intersection + sed -e 's/^/ # /;' fb.GCF_000151845.1.chainSynGCF_001704415.2Link.txt + # 1267672512 bases of 2198284804 (57.666%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/000/151/845/GCF_000151845.1/GCF_000151845.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/000/151/845/GCF_000151845.1/GCF_000151845.1.chrom.sizes.txt" \ + GCF_000151845.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 200m30.570s + + sed -e 's/^/ # /;' fb.GCF_000151845.1.chainRBest.GCF_001704415.2.txt + # 1266996984 bases of 2198284804 (57.636%) in intersection + +############################################################################## + +############################################################################## +# LASTZ goat GCF_001704415.2 vs. harbor seal GCF_004348235.1 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_004348235.1.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_004348235.1.2026-04-17 + + printf '# harbor seal GCF_004348235.1 vs. goat GCF_001704415.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: goat 2016-08-24 GCF_001704415.2_ARS1.2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: harbor seal 2019-02-11 GCF_004348235.1_GSC_HSeal_1.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/004/348/235/GCF_004348235.1/GCF_004348235.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/004/348/235/GCF_004348235.1/GCF_004348235.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_004348235.1.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCF_004348235.1_GSC_HSeal_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 883m1.668s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_004348235.1Link.txt + # 1531490545 bases of 2922617086 (52.401%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_004348235.1Link.txt + # 1399910376 bases of 2922617086 (47.899%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/004/348/235/GCF_004348235.1/GCF_004348235.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/004/348/235/GCF_004348235.1/GCF_004348235.1.chrom.sizes.txt" \ + GCF_001704415.2 GCF_004348235.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 162m43.940s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_004348235.1.txt + # 1390466297 bases of 2922617086 (47.576%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/004/348/235/GCF_004348235.1_GSC_HSeal_1.0/trackData/blastz.GCF_001704415.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCF_004348235.1_GSC_HSeal_1.0 /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_004348235.1.2026-04-17/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 84m21.492s + + sed -e 's/^/ # /;' fb.GCF_004348235.1.chainGCF_001704415.2Link.txt + # 1429597500 bases of 2362163281 (60.521%) in intersection + sed -e 's/^/ # /;' fb.GCF_004348235.1.chainSynGCF_001704415.2Link.txt + # 1381434570 bases of 2362163281 (58.482%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/004/348/235/GCF_004348235.1/GCF_004348235.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/004/348/235/GCF_004348235.1/GCF_004348235.1.chrom.sizes.txt" \ + GCF_004348235.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 143m37.863s + + sed -e 's/^/ # /;' fb.GCF_004348235.1.chainRBest.GCF_001704415.2.txt + # 1388354381 bases of 2362163281 (58.775%) in intersection + +############################################################################## + +############################################################################## +# LASTZ goat GCF_001704415.2 vs. dog GCF_014441545.1 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_014441545.1.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_014441545.1.2026-04-17 + + printf '# dog GCF_014441545.1 vs. goat GCF_001704415.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: goat 2016-08-24 GCF_001704415.2_ARS1.2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: dog 2020-09-03 GCF_014441545.1_ROS_Cfam_1.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_014441545.1.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCF_014441545.1_ROS_Cfam_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 873m36.535s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_014441545.1Link.txt + # 1418970257 bases of 2922617086 (48.551%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_014441545.1Link.txt + # 1363646433 bases of 2922617086 (46.658%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ + GCF_001704415.2 GCF_014441545.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 167m51.935s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_014441545.1.txt + # 1350659616 bases of 2922617086 (46.214%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/014/441/545/GCF_014441545.1_ROS_Cfam_1.0/trackData/blastz.GCF_001704415.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCF_014441545.1_ROS_Cfam_1.0 /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_014441545.1.2026-04-17/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 72m56.684s + + sed -e 's/^/ # /;' fb.GCF_014441545.1.chainGCF_001704415.2Link.txt + # 1405016159 bases of 2396858295 (58.619%) in intersection + sed -e 's/^/ # /;' fb.GCF_014441545.1.chainSynGCF_001704415.2Link.txt + # 1358767342 bases of 2396858295 (56.690%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ + GCF_014441545.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 170m34.864s + + sed -e 's/^/ # /;' fb.GCF_014441545.1.chainRBest.GCF_001704415.2.txt + # 1349933474 bases of 2396858295 (56.321%) in intersection + +############################################################################## + +############################################################################## +# LASTZ goat GCF_001704415.2 vs. Bactrian camel GCF_048773025.1 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_048773025.1.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_048773025.1.2026-04-17 + + printf '# Bactrian camel GCF_048773025.1 vs. goat GCF_001704415.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: goat 2016-08-24 GCF_001704415.2_ARS1.2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Bactrian camel 2025-03-21 GCF_048773025.1_ASM4877302v1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/048/773/025/GCF_048773025.1/GCF_048773025.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/048/773/025/GCF_048773025.1/GCF_048773025.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_048773025.1.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCF_048773025.1_ASM4877302v1 -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 1007m23.680s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_048773025.1Link.txt + # 1676392977 bases of 2922617086 (57.359%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_048773025.1Link.txt + # 1505672120 bases of 2922617086 (51.518%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/048/773/025/GCF_048773025.1/GCF_048773025.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/048/773/025/GCF_048773025.1/GCF_048773025.1.chrom.sizes.txt" \ + GCF_001704415.2 GCF_048773025.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 562m48.448s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_048773025.1.txt + # 1503700125 bases of 2922617086 (51.450%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/048/773/025/GCF_048773025.1_ASM4877302v1/trackData/blastz.GCF_001704415.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_001704415.2_ARS1.2 -qAsmId GCF_048773025.1_ASM4877302v1 /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/lastzGCF_048773025.1.2026-04-17/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 150m22.502s + + sed -e 's/^/ # /;' fb.GCF_048773025.1.chainGCF_001704415.2Link.txt + # 1698506027 bases of 2473918224 (68.657%) in intersection + sed -e 's/^/ # /;' fb.GCF_048773025.1.chainSynGCF_001704415.2Link.txt + # 1515060622 bases of 2473918224 (61.241%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -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" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/048/773/025/GCF_048773025.1/GCF_048773025.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/048/773/025/GCF_048773025.1/GCF_048773025.1.chrom.sizes.txt" \ + GCF_048773025.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 517m51.907s + + sed -e 's/^/ # /;' fb.GCF_048773025.1.chainRBest.GCF_001704415.2.txt + # 1497324732 bases of 2473918224 (60.524%) in intersection + +############################################################################## + +############################################################################## +# LASTZ Chinese hamster GCF_003668045.3 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/003/668/045/GCF_003668045.3_CriGri-PICRH-1.0/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/003/668/045/GCF_003668045.3_CriGri-PICRH-1.0/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 vs. Chinese hamster GCF_003668045.3 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Chinese hamster 2020-06-11 GCF_003668045.3_CriGri-PICRH-1.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/003/668/045/GCF_003668045.3/GCF_003668045.3.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/003/668/045/GCF_003668045.3/GCF_003668045.3.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/GCF/003/668/045/GCF_003668045.3_CriGri-PICRH-1.0/trackData/lastzGCF_001704415.2.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_003668045.3_CriGri-PICRH-1.0 -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 813m11.712s + + sed -e 's/^/ # /;' fb.GCF_003668045.3.chainGCF_001704415.2Link.txt + # 749837921 bases of 2366634374 (31.684%) in intersection + sed -e 's/^/ # /;' fb.GCF_003668045.3.chainSynGCF_001704415.2Link.txt + # 700596755 bases of 2366634374 (29.603%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/003/668/045/GCF_003668045.3/GCF_003668045.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/003/668/045/GCF_003668045.3/GCF_003668045.3.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" \ + GCF_003668045.3 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 240m5.572s + + sed -e 's/^/ # /;' fb.GCF_003668045.3.chainRBest.GCF_001704415.2.txt + # 712023509 bases of 2366634374 (30.086%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCF_003668045.3.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_003668045.3_CriGri-PICRH-1.0 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCF/003/668/045/GCF_003668045.3_CriGri-PICRH-1.0/trackData/lastzGCF_001704415.2.2026-04-17/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 47m14.866s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_003668045.3Link.txt + # 743507026 bases of 2922617086 (25.440%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_003668045.3Link.txt + # 701520802 bases of 2922617086 (24.003%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/003/668/045/GCF_003668045.3/GCF_003668045.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/003/668/045/GCF_003668045.3/GCF_003668045.3.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 GCF_003668045.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 227m24.139s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_003668045.3.txt + # 711120349 bases of 2922617086 (24.332%) in intersection + +############################################################################## + +############################################################################## +# LASTZ Donkey GCF_016077325.2 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/016/077/325/GCF_016077325.2_ASM1607732v2/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/016/077/325/GCF_016077325.2_ASM1607732v2/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 vs. Donkey GCF_016077325.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Donkey 2021-10-14 GCF_016077325.2_ASM1607732v2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/016/077/325/GCF_016077325.2/GCF_016077325.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/016/077/325/GCF_016077325.2/GCF_016077325.2.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/GCF/016/077/325/GCF_016077325.2_ASM1607732v2/trackData/lastzGCF_001704415.2.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_016077325.2_ASM1607732v2 -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 866m31.335s + + sed -e 's/^/ # /;' fb.GCF_016077325.2.chainGCF_001704415.2Link.txt + # 1622728903 bases of 2431907375 (66.727%) in intersection + sed -e 's/^/ # /;' fb.GCF_016077325.2.chainSynGCF_001704415.2Link.txt + # 1491658146 bases of 2431907375 (61.337%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/016/077/325/GCF_016077325.2/GCF_016077325.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/016/077/325/GCF_016077325.2/GCF_016077325.2.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" \ + GCF_016077325.2 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 281m56.588s + + sed -e 's/^/ # /;' fb.GCF_016077325.2.chainRBest.GCF_001704415.2.txt + # 1472919658 bases of 2431907375 (60.566%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCF_016077325.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_016077325.2_ASM1607732v2 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCF/016/077/325/GCF_016077325.2_ASM1607732v2/trackData/lastzGCF_001704415.2.2026-04-17/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 105m23.636s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_016077325.2Link.txt + # 1564985167 bases of 2922617086 (53.547%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_016077325.2Link.txt + # 1483751552 bases of 2922617086 (50.768%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/016/077/325/GCF_016077325.2/GCF_016077325.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/016/077/325/GCF_016077325.2/GCF_016077325.2.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 GCF_016077325.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 271m43.996s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_016077325.2.txt + # 1476278377 bases of 2922617086 (50.512%) in intersection + +############################################################################## + +############################################################################## +# LASTZ domestic cat GCF_018350175.1 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/018/350/175/GCF_018350175.1_F.catus_Fca126_mat1.0/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/018/350/175/GCF_018350175.1_F.catus_Fca126_mat1.0/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 vs. domestic cat GCF_018350175.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: domestic cat 2021-05-13 GCF_018350175.1_F.catus_Fca126_mat1.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/018/350/175/GCF_018350175.1/GCF_018350175.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/018/350/175/GCF_018350175.1/GCF_018350175.1.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/GCF/018/350/175/GCF_018350175.1_F.catus_Fca126_mat1.0/trackData/lastzGCF_001704415.2.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_018350175.1_F.catus_Fca126_mat1.0 -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 837m34.397s + + sed -e 's/^/ # /;' fb.GCF_018350175.1.chainGCF_001704415.2Link.txt + # 1417422563 bases of 2425747038 (58.432%) in intersection + sed -e 's/^/ # /;' fb.GCF_018350175.1.chainSynGCF_001704415.2Link.txt + # 1373655407 bases of 2425747038 (56.628%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/018/350/175/GCF_018350175.1/GCF_018350175.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/018/350/175/GCF_018350175.1/GCF_018350175.1.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" \ + GCF_018350175.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 243m8.952s + + sed -e 's/^/ # /;' fb.GCF_018350175.1.chainRBest.GCF_001704415.2.txt + # 1377248417 bases of 2425747038 (56.776%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCF_018350175.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_018350175.1_F.catus_Fca126_mat1.0 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCF/018/350/175/GCF_018350175.1_F.catus_Fca126_mat1.0/trackData/lastzGCF_001704415.2.2026-04-17/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 73m10.186s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_018350175.1Link.txt + # 1449186142 bases of 2922617086 (49.585%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_018350175.1Link.txt + # 1393553634 bases of 2922617086 (47.682%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/018/350/175/GCF_018350175.1/GCF_018350175.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/018/350/175/GCF_018350175.1/GCF_018350175.1.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 GCF_018350175.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 249m28.147s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_018350175.1.txt + # 1378562445 bases of 2922617086 (47.169%) in intersection + +############################################################################## + +############################################################################## +# LASTZ water buffalo GCF_019923935.1 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 vs. water buffalo GCF_019923935.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.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/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzGCF_001704415.2.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_019923935.1_NDDB_SH_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 1095m52.936s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainGCF_001704415.2Link.txt + # 2369413736 bases of 2622460639 (90.351%) in intersection + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainSynGCF_001704415.2Link.txt + # 2277890709 bases of 2622460639 (86.861%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.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" \ + GCF_019923935.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 298m52.169s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainRBest.GCF_001704415.2.txt + # 2280827808 bases of 2622460639 (86.973%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCF_019923935.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_019923935.1_NDDB_SH_1 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastzGCF_001704415.2.2026-04-17/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 162m57.521s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_019923935.1Link.txt + # 2388829228 bases of 2922617086 (81.736%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_019923935.1Link.txt + # 2311168206 bases of 2922617086 (79.079%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.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 GCF_019923935.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 244m18.452s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_019923935.1.txt + # 2282586463 bases of 2922617086 (78.101%) in intersection + +############################################################################## + +############################################################################## +# LASTZ tammar wallaby GCF_028372415.1 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/028/372/415/GCF_028372415.1_mMacEug1.pri_v2/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/028/372/415/GCF_028372415.1_mMacEug1.pri_v2/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 vs. tammar wallaby GCF_028372415.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: tammar wallaby 2023-02-06 GCF_028372415.1_mMacEug1.pri_v2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/028/372/415/GCF_028372415.1/GCF_028372415.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/028/372/415/GCF_028372415.1/GCF_028372415.1.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/GCF/028/372/415/GCF_028372415.1_mMacEug1.pri_v2/trackData/lastzGCF_001704415.2.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_028372415.1_mMacEug1.pri_v2 -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 833m9.640s + + sed -e 's/^/ # /;' fb.GCF_028372415.1.chainGCF_001704415.2Link.txt + # 254285983 bases of 3447464908 (7.376%) in intersection + sed -e 's/^/ # /;' fb.GCF_028372415.1.chainSynGCF_001704415.2Link.txt + # 83229974 bases of 3447464908 (2.414%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/028/372/415/GCF_028372415.1/GCF_028372415.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/028/372/415/GCF_028372415.1/GCF_028372415.1.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" \ + GCF_028372415.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 1684m45.083s + + sed -e 's/^/ # /;' fb.GCF_028372415.1.chainRBest.GCF_001704415.2.txt + # 191434043 bases of 3447464908 (5.553%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCF_028372415.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_028372415.1_mMacEug1.pri_v2 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCF/028/372/415/GCF_028372415.1_mMacEug1.pri_v2/trackData/lastzGCF_001704415.2.2026-04-17/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 30m15.050s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_028372415.1Link.txt + # 227696745 bases of 2922617086 (7.791%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_028372415.1Link.txt + # 82641740 bases of 2922617086 (2.828%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/028/372/415/GCF_028372415.1/GCF_028372415.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/028/372/415/GCF_028372415.1/GCF_028372415.1.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 GCF_028372415.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 1521m49.314s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_028372415.1.txt + # 192076089 bases of 2922617086 (6.572%) in intersection + +############################################################################## + +############################################################################## +# LASTZ sugar glider GCF_028583685.1 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/028/583/685/GCF_028583685.1_PetGlider_PUasm1.0/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/028/583/685/GCF_028583685.1_PetGlider_PUasm1.0/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 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: 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/GCF/028/583/685/GCF_028583685.1_PetGlider_PUasm1.0/trackData/lastzGCF_001704415.2.2026-04-17 +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_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 797m25.351s + + sed -e 's/^/ # /;' fb.GCF_028583685.1.chainGCF_001704415.2Link.txt + # 252732381 bases of 3464720375 (7.294%) in intersection + sed -e 's/^/ # /;' fb.GCF_028583685.1.chainSynGCF_001704415.2Link.txt + # 79946144 bases of 3464720375 (2.307%) 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/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" \ + GCF_028583685.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 433m42.682s + + sed -e 's/^/ # /;' fb.GCF_028583685.1.chainRBest.GCF_001704415.2.txt + # 190613203 bases of 3464720375 (5.502%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/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_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCF/028/583/685/GCF_028583685.1_PetGlider_PUasm1.0/trackData/lastzGCF_001704415.2.2026-04-17/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 16m3.821s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_028583685.1Link.txt + # 226636931 bases of 2922617086 (7.755%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_028583685.1Link.txt + # 77949334 bases of 2922617086 (2.667%) 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/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 GCF_028583685.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 335m49.537s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_028583685.1.txt + # 191709735 bases of 2922617086 (6.560%) in intersection + +############################################################################## + +############################################################################## +# LASTZ Tasmanian devil GCF_902635505.1 vs. goat GCF_001704415.2 +# (DONE - 2026-04-17 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/902/635/505/GCF_902635505.1_mSarHar1.11/trackData/lastzGCF_001704415.2.2026-04-17 + cd /hive/data/genomes/asmHubs/allBuild/GCF/902/635/505/GCF_902635505.1_mSarHar1.11/trackData/lastzGCF_001704415.2.2026-04-17 + + printf '# goat GCF_001704415.2 vs. Tasmanian devil GCF_902635505.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Tasmanian devil 2019-11-07 GCF_902635505.1_mSarHar1.11 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/902/635/505/GCF_902635505.1/GCF_902635505.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/902/635/505/GCF_902635505.1/GCF_902635505.1.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/GCF/902/635/505/GCF_902635505.1_mSarHar1.11/trackData/lastzGCF_001704415.2.2026-04-17 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_902635505.1_mSarHar1.11 -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 1095m22.944s + + sed -e 's/^/ # /;' fb.GCF_902635505.1.chainGCF_001704415.2Link.txt + # 193104779 bases of 3086674442 (6.256%) in intersection + sed -e 's/^/ # /;' fb.GCF_902635505.1.chainSynGCF_001704415.2Link.txt + # 75455741 bases of 3086674442 (2.445%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/902/635/505/GCF_902635505.1/GCF_902635505.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/902/635/505/GCF_902635505.1/GCF_902635505.1.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" \ + GCF_902635505.1 GCF_001704415.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 1298m14.550s + + sed -e 's/^/ # /;' fb.GCF_902635505.1.chainRBest.GCF_001704415.2.txt + # 174010223 bases of 3086674442 (5.637%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/001/704/415/GCF_001704415.2_ARS1.2/trackData/blastz.GCF_902635505.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_902635505.1_mSarHar1.11 -qAsmId GCF_001704415.2_ARS1.2 /hive/data/genomes/asmHubs/allBuild/GCF/902/635/505/GCF_902635505.1_mSarHar1.11/trackData/lastzGCF_001704415.2.2026-04-17/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 17m31.975s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainGCF_902635505.1Link.txt + # 193674784 bases of 2922617086 (6.627%) in intersection + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainSynGCF_902635505.1Link.txt + # 75345697 bases of 2922617086 (2.578%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/902/635/505/GCF_902635505.1/GCF_902635505.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/902/635/505/GCF_902635505.1/GCF_902635505.1.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 GCF_902635505.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 1453m22.479s + + sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.GCF_902635505.1.txt + # 173486700 bases of 2922617086 (5.936%) in intersection + +##############################################################################