4961f406b518a415fdc2de506c97a940bf915aca gperez2 Mon Jan 31 15:56:15 2022 -0800 mummichog GCF_011125445.2 vs. mummichog GCF_000826765.1 lastz/chain/net run for user, refs #28365 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 5ca1574..07c4425 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -1469,15 +1469,123 @@ -querySizes="/hive/data/genomes/asmHubs/GCF/014/441/545/GCF_014441545.1/GCF_014441545.1.chrom.sizes.txt" \ \ canFam3 GCF_014441545.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 66m14.435s sed -e 's/^/ # /;' fb.canFam3.chainRBest.GCF_014441545.1.txt # 2307013600 bases of 2410976875 (95.688%) in intersection ############################################################################## real 758m9.174s user 0m1.449s sys 0m1.346s +############################################################################## +# LASTZ mummichog GCF_011125445.2 vs. mummichog GCF_000826765.1 (DONE - 2022-01-21 - Gerardo) + +# should be able to run this from anywhere, this time it was run from: + cd kent/src/hg/utils/automation + + time (~/kent/src/hg/utils/automation/pairLastz.sh \ + GCF_011125445.2_MU-UCD_Fhet_4.1 GCF_000826765.1_Fundulus_heteroclitus-3.0.2 other other) \ + > GCF011125445_GCF000826765_20220121.log 2>&1 & + # check the total time +grep -w real GCF011125445_GCF000826765_20220121.log | tail -1 | sed -e 's/^/ # /;' + # real 1621m36.194s + + # this GCF011125445_GCF000826765_20220121.log log file happens to have a copy of the make doc, as well + # as the copy of the make doc left in the target assembly directory: +# /hive/data/genomes/asmHubs/allBuild/GCF/011/125/445/GCF_011125445.2_MU-UCD_Fhet_4.1/trackData/lastzGCF_000826765.1.2022-01-21/makeDoc.txt + + # this command outputs this makeDoc text: + + cat kent/src/hg/utils/automation/GCF011125445_GCF000826765_20220121.log + +############################################################################## +# LASTZ mummichog GCF_011125445.2 vs. mummichog GCF_000826765.1 +# (DONE - 2022-01-21 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/011/125/445/GCF_011125445.2_MU-UCD_Fhet_4.1/trackData/lastzGCF_000826765.1.2022-01-21 + cd /hive/data/genomes/asmHubs/allBuild/GCF/011/125/445/GCF_011125445.2_MU-UCD_Fhet_4.1/trackData/lastzGCF_000826765.1.2022-01-21 + + printf '# mummichog GCF_000826765.1 vs. mummichog GCF_011125445.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: mummichog GCF_011125445.2 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: mummichog GCF_000826765.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/011/125/445/GCF_011125445.2_MU-UCD_Fhet_4.1/trackData/lastzGCF_000826765.1.2022-01-21 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_011125445.2_MU-UCD_Fhet_4.1 -qAsmId GCF_000826765.1_Fundulus_heteroclitus-3.0.2 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 755m29.866s + + sed -e 's/^/ # /;' fb.GCF_011125445.2.chainGCF_000826765.1Link.txt + # 1069310182 bases of 1203505739 (88.850%) in intersection + sed -e 's/^/ # /;' fb.GCF_011125445.2.chainSynGCF_000826765.1Link.txt + # 885838715 bases of 1203505739 (73.605%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.chrom.sizes.txt" \ + GCF_011125445.2 GCF_000826765.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 86m1.406s + + sed -e 's/^/ # /;' fb.GCF_011125445.2.chainRBest.GCF_000826765.1.txt + # 858755159 bases of 1203505739 (71.354%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/000/826/765/GCF_000826765.1_Fundulus_heteroclitus-3.0.2/trackData/blastz.GCF_011125445.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_011125445.2_MU-UCD_Fhet_4.1 -qAsmId GCF_000826765.1_Fundulus_heteroclitus-3.0.2 /hive/data/genomes/asmHubs/allBuild/GCF/011/125/445/GCF_011125445.2_MU-UCD_Fhet_4.1/trackData/lastzGCF_000826765.1.2022-01-21/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 706m8.827s + + sed -e 's/^/ # /;' fb.GCF_000826765.1.chainGCF_011125445.2Link.txt + # 906492141 bases of 1021898560 (88.707%) in intersection + sed -e 's/^/ # /;' fb.GCF_000826765.1.chainSynGCF_011125445.2Link.txt + # 852990578 bases of 1021898560 (83.471%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/011/125/445/GCF_011125445.2/GCF_011125445.2.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/000/826/765/GCF_000826765.1/GCF_000826765.1.chrom.sizes.txt" \ + GCF_000826765.1 GCF_011125445.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 73m55.254s + + sed -e 's/^/ # /;' fb.GCF_000826765.1.chainRBest.GCF_011125445.2.txt + # 865608764 bases of 1021898560 (84.706%) in intersection + +############################################################################## + +real 1621m36.194s +user 0m2.046s +sys 0m2.922s