8e4313e37e6c53753fcc42e5d068b05250db629b gperez2 Wed Dec 22 11:53:51 2021 -0800 sheep GCF_002742125.1 vs. mm39 lastz/chain/net run for user, refs #28668 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 9d994c5..1a1c5e0 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -1258,15 +1258,121 @@ -querySizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/016/772/045/GCF_016772045.1/GCF_016772045.1.chrom.sizes.txt" \ GCF_016772045.1 GCF_002742125.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 81m52.743s sed -e 's/^/ # /;' fb.GCF_016772045.1.chainRBest.GCF_002742125.1.txt # 2611860239 bases of 2628146905 (99.380%) in intersection real 2656m30.586s user 0m1.556s sys 0m1.520s +############################################################################## +# LASTZ sheep GCF_002742125.1 vs. Mouse Mm39 (DONE - 2021-12-21 - 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_002742125.1_Oar_rambouillet_v1.0 mm39 mammal mammal) \ + > GCF002742125_mm39_20211221.log 2>&1 & + # check the total time +grep -w real GCF002742125_mm39_20211221.log | tail -1 | sed -e 's/^/ # /;' + # real 1011m49.661s + + # this GCF002742125_mm39_20211221.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/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzMm39.2021-12-21/makeDoc.txt + + # this command outputs this makeDoc text: + + cat ~/kent/src/hg/utils/automation/GCF002742125_mm39_20211221.log + +############################################################################## +# LASTZ sheep GCF_002742125.1 vs. Mouse Mm39 +# (DONE - 2021-12-21 - Gerardo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzMm39.2021-12-21 + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzMm39.2021-12-21 + + printf '# Mouse Mm39 vs. sheep GCF_002742125.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: sheep GCF_002742125.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Mouse Mm39 +SEQ2_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ2_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzMm39.2021-12-21 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_002742125.1_Oar_rambouillet_v1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 230m6.460s + + sed -e 's/^/ # /;' fb.GCF_002742125.1.chainMm39Link.txt + # 724687034 bases of 2869914396 (25.251%) in intersection + sed -e 's/^/ # /;' fb.GCF_002742125.1.chainSynMm39Link.txt + # 661688482 bases of 2869914396 (23.056%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ + \ + GCF_002742125.1 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 362m25.103s + + sed -e 's/^/ # /;' fb.GCF_002742125.1.chainRBest.Mm39.txt + # 660762547 bases of 2869914396 (23.024%) in intersection + + ### and for the swap + + cd /hive/data/genomes/mm39/bed/blastz.GCF_002742125.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_002742125.1_Oar_rambouillet_v1.0 /hive/data/genomes/asmHubs/allBuild/GCF/002/742/125/GCF_002742125.1_Oar_rambouillet_v1.0/trackData/lastzMm39.2021-12-21/DEF -swapDir=`pwd` \ + -syntenicNet -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > swap.log 2>&1 + + grep -w real swap.log | sed -e 's/^/ # /;' + # real 92m24.630s + + sed -e 's/^/ # /;' fb.mm39.chainGCF_002742125.1Link.txt + # 695954726 bases of 2728222451 (25.509%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCF_002742125.1Link.txt + # 646953218 bases of 2728222451 (23.713%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/742/125/GCF_002742125.1/GCF_002742125.1.chrom.sizes.txt" \ + \ + mm39 GCF_002742125.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 326m52.826s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCF_002742125.1.txt + # 660752248 bases of 2728222451 (24.219%) in intersection + + +real 1011m49.661s +user 0m1.668s +sys 0m1.378s +