0bcfab505e3e3fa981b3d220f0354128e7a8a2df gperez2 Sun Sep 15 16:11:48 2024 -0700 violet copper butterfly (GCA_963853865.1) to butterfly C.glycerion (GCA_963855885.1) lastz/chain/net run for user, refs #33991 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 74f30b5..6b32272 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -2787,31 +2787,114 @@ -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 oviAri4) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 180m47.478s sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.OviAri4.txt # 2474132806 bases of 2922617086 (84.655%) in intersection ############################################################################## ### elapsed time: 45h 34m 01s Sun Jun 9 08:32:19 PDT 2024 ################################################################## +# LASTZ violet copper GCA_963853865.1 vs. butterflies GCA_963855885.1 +# (DONE - 2024-06-21 - Gerardo) + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/963/853/865/GCA_963853865.1_ilHelHell1.1/trackData/lastzGCA_963855885.1.2024-06-21 + cd /hive/data/genomes/asmHubs/allBuild/GCA/963/853/865/GCA_963853865.1_ilHelHell1.1/trackData/lastzGCA_963855885.1.2024-06-21 + + printf '# butterflies GCA_963855885.1 vs. violet copper GCA_963853865.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: violet copper 2023-12-13 GCA_963853865.1_ilHelHell1.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/963/853/865/GCA_963853865.1/GCA_963853865.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/963/853/865/GCA_963853865.1/GCA_963853865.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: butterflies 2023-12-15 GCA_963855885.1_ilCoeGlyc1.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/963/855/885/GCA_963855885.1/GCA_963855885.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/963/855/885/GCA_963855885.1/GCA_963855885.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCA/963/853/865/GCA_963853865.1_ilHelHell1.1/trackData/lastzGCA_963855885.1.2024-06-21 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCA_963853865.1_ilHelHell1.1 -qAsmId GCA_963855885.1_ilCoeGlyc1.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 22m20.850s + + sed -e 's/^/ # /;' fb.GCA_963853865.1.chainGCA_963855885.1Link.txt + # 74002762 bases of 547321747 (13.521%) in intersection + sed -e 's/^/ # /;' fb.GCA_963853865.1.chainSynGCA_963855885.1Link.txt + # 32827319 bases of 547321747 (5.998%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCA/963/853/865/GCA_963853865.1/GCA_963853865.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/963/853/865/GCA_963853865.1/GCA_963853865.1.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/963/855/885/GCA_963855885.1/GCA_963855885.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/963/855/885/GCA_963855885.1/GCA_963855885.1.chrom.sizes.txt" \ + GCA_963853865.1 GCA_963855885.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 20m47.571s + + sed -e 's/^/ # /;' fb.GCA_963853865.1.chainRBest.GCA_963855885.1.txt + # 42799072 bases of 547321747 (7.820%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/963/855/885/GCA_963855885.1_ilCoeGlyc1.1/trackData/blastz.GCA_963853865.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCA_963853865.1_ilHelHell1.1 -qAsmId GCA_963855885.1_ilCoeGlyc1.1 /hive/data/genomes/asmHubs/allBuild/GCA/963/853/865/GCA_963853865.1_ilHelHell1.1/trackData/lastzGCA_963855885.1.2024-06-21/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 11m50.695s + + sed -e 's/^/ # /;' fb.GCA_963855885.1.chainGCA_963853865.1Link.txt + # 67947875 bases of 457736400 (14.844%) in intersection + sed -e 's/^/ # /;' fb.GCA_963855885.1.chainSynGCA_963853865.1Link.txt + # 36202978 bases of 457736400 (7.909%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCA/963/853/865/GCA_963853865.1/GCA_963853865.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/963/853/865/GCA_963853865.1/GCA_963853865.1.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCA/963/855/885/GCA_963855885.1/GCA_963855885.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/963/855/885/GCA_963855885.1/GCA_963855885.1.chrom.sizes.txt" \ + GCA_963855885.1 GCA_963853865.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 20m44.501s + + sed -e 's/^/ # /;' fb.GCA_963855885.1.chainRBest.GCA_963853865.1.txt + # 42397910 bases of 457736400 (9.263%) in intersection + +real 75m47.883s +user 0m2.731s +sys 0m3.078s ############################################################################## # LASTZ domestic cattle GCF_002263795.3 vs. Bactrian camel GCF_000767855.1 # (DONE - 2024-08-29 - jairo) mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_000767855.1.2024-08-29 cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_000767855.1.2024-08-29 printf '# Bactrian camel GCF_000767855.1 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