77740770d513278f03c8cb1eac5f02c83c6c26c4 gperez2 Thu Feb 10 16:40:31 2022 -0800 Correcting makedoc location for taeGut2 vs. geoFor1 lastz/chain/net run for user, refs #28840 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 3b908bd..fb4bf6b 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -1578,116 +1578,15 @@ -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 ############################################################################## -# LASTZ Zebra finch TaeGut2 vs. Medium ground finch GeoFor1 (DONE - 2022-02-03 -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 \ - taeGut2 geoFor1 other other) \ - > zebraFinch_medFinch_20220202_secondTime.log 2>&1 & - # check the total time -grep -w real zebraFinch_medFinch_20220202_secondTime.log | tail -1 | sed -e 's/^/ # /;' - # real 107m34.019s - - # this zebraFinch_medFinch_20220202_secondTime.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/taeGut2/bed/lastzGeoFor1.2022-02-02/makeDoc.txt - - # this command outputs this makeDoc text: - - cat kent/src/hg/utils/automation/zebraFinch_medFinch_20220202_secondTime.log - -############################################################################## -# LASTZ Zebra finch TaeGut2 vs. Medium ground finch GeoFor1 -# (DONE - 2022-02-03 - Gerardo) - - mkdir /hive/data/genomes/taeGut2/bed/lastzGeoFor1.2022-02-02 - cd /hive/data/genomes/taeGut2/bed/lastzGeoFor1.2022-02-02 - - printf '# Medium ground finch GeoFor1 vs. Zebra finch TaeGut2 -BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz - -# TARGET: Zebra finch TaeGut2 -SEQ1_DIR=/hive/data/genomes/taeGut2/taeGut2.2bit -SEQ1_LEN=/hive/data/genomes/taeGut2/chrom.sizes -SEQ1_CHUNK=20000000 -SEQ1_LAP=10000 -SEQ1_LIMIT=40 - -# QUERY: Medium ground finch GeoFor1 -SEQ2_DIR=/hive/data/genomes/geoFor1/geoFor1.2bit -SEQ2_LEN=/hive/data/genomes/geoFor1/chrom.sizes -SEQ2_CHUNK=20000000 -SEQ2_LAP=0 -SEQ2_LIMIT=100 - -BASE=/hive/data/genomes/taeGut2/bed/lastzGeoFor1.2022-02-02 -TMPDIR=/dev/shm - -' > DEF - - time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -verbose=2 `pwd`/DEF -syntenicNet \ - -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ - -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 - grep -w real do.log | sed -e 's/^/ # /;' - # real 159m10.037s - - sed -e 's/^/ # /;' fb.taeGut2.chainGeoFor1Link.txt - # 1125215195 bases of 1222864691 (92.015%) in intersection - sed -e 's/^/ # /;' fb.taeGut2.chainSynGeoFor1Link.txt - # 1024055100 bases of 1222864691 (83.742%) in intersection - - time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ - \ - \ - taeGut2 geoFor1) > rbest.log 2>&1 - - grep -w real rbest.log | sed -e 's/^/ # /;' - - sed -e 's/^/ # /;' fb.taeGut2.chainRBest.GeoFor1.txt - - ### and for the swap - - cd /hive/data/genomes/geoFor1/bed/blastz.taeGut2.swap - - time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -swap -verbose=2 \ - /hive/data/genomes/taeGut2/bed/lastzGeoFor1.2022-02-02/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 42m46.900s - - sed -e 's/^/ # /;' fb.geoFor1.chainTaeGut2Link.txt - # 954457151 bases of 1041286029 (91.661%) in intersection - sed -e 's/^/ # /;' fb.geoFor1.chainSynTaeGut2Link.txt - # 912902982 bases of 1041286029 (87.671%) in intersection -\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ - \ - \ - geoFor1 taeGut2) > rbest.log 2>&1 - - grep -w real rbest.log | sed -e 's/^/ # /;' - # real 64m46.642s - - sed -e 's/^/ # /;' fb.geoFor1.chainRBest.TaeGut2.txt - # 919870835 bases of 1041286029 (88.340%) in intersection - -############################################################################## - -real 107m34.019s -user 0m1.109s -sys 0m1.771s