9e7949fb6dd9cbb6379327b52e762cdecde5341a hiram Thu Oct 7 09:47:15 2021 -0700 finish off lastz/chain/net procedure no redmine diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index df51f1b..4db359e 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -1,98 +1,104 @@ - ############################################################################## -# LASTZ tardigrades GCA_001949185.1 (DONE - 2021-10-06 - Hiram) +# LASTZ tardigrades GCA_001949185.1 (DONE - 2021-10-06 - Gerardo) # should be able to run this from anywhere, this time it was run from: cd kent/src/hg/utils/automation - time (/hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06/run.sh) \ - >> /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06/do.log 2>&1 + time (~/kent/src/hg/utils/automation/pairLastz.sh \ + GCA_001949185.1_Rvar_4.0 GCA_002082055.1_nHd_3.1 other other) \ + > liftOverTest.log 2>&1 + # check the total time + grep -w real liftOverTest.log | tail -1 | sed -e 's/^/ # /;' + # real 15m52.438s - grep -w real do.log | tail -1 | sed -e 's/^/ # /;' - # real 10m31.512s + # this liftOverTest 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/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06/makeDoc.txt # this command outputs this makeDoc text: cat kent/src/hg/utils/automation/liftOverTest.log ############################################################################## -# LASTZ tardigrades GCA_001949185.1 vs. tardigrades GCA_002082055.1 (DONE - 2021-10-06 - Hiram) +# LASTZ tardigrades GCA_001949185.1 vs. tardigrades GCA_002082055.1 +# (DONE - 2021-10-06 - Gerardo) + mkdir /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06 cd /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06 printf '# tardigrades GCA_002082055.1 vs. tardigrades GCA_001949185.1 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: tardigrades GCA_001949185.1 SEQ1_DIR=/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.2bit SEQ1_LEN=/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.chrom.sizes.txt SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=40 # QUERY: tardigrades GCA_002082055.1 SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.2bit SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.chrom.sizes.txt SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=100 BASE=/hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06 TMPDIR=/dev/shm ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ -tAsmId GCA_001949185.1_Rvar_4.0 -qAsmId GCA_002082055.1_nHd_3.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ -chainMinScore=5000 -chainLinearGap=loose) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' # real 10m31.512s sed -e 's/^/ # /;' fb.GCA_001949185.1.chainGCA_002082055.1Link.txt # 14450772 bases of 55842812 (25.878%) in intersection sed -e 's/^/ # /;' fb.GCA_001949185.1.chainSynGCA_002082055.1Link.txt # 6694962 bases of 55842812 (11.989%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -target2Bit="/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.chrom.sizes.txt" \ -query2Bit="/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.chrom.sizes.txt" \ GCA_001949185.1 GCA_002082055.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 1m39.278s sed -e 's/^/ # /;' fb.GCA_001949185.1.chainRBest.GCA_002082055.1.txt # 12952644 bases of 55842812 (23.195%) in intersection ### and for the swap cd /hive/data/genomes/asmHubs/allBuild/GCA/002/082/055/GCA_002082055.1_nHd_3.1/trackData/blastz.GCA_001949185.1.swap time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ -tAsmId GCA_001949185.1_Rvar_4.0 -qAsmId GCA_002082055.1_nHd_3.1 /hive/data/genomes/asmHubs/allBuild/GCA/001/949/185/GCA_001949185.1_Rvar_4.0/trackData/lastzGCA_002082055.1.2021-10-06/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 2m1.276s sed -e 's/^/ # /;' fb.GCA_002082055.1.chainGCA_001949185.1Link.txt # 15159345 bases of 104154999 (14.555%) in intersection sed -e 's/^/ # /;' fb.GCA_002082055.1.chainSynGCA_001949185.1Link.txt # 7022280 bases of 104154999 (6.742%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCA/001/949/185/GCA_001949185.1/GCA_001949185.1.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/002/082/055/GCA_002082055.1/GCA_002082055.1.chrom.sizes.txt" \ GCA_002082055.1 GCA_001949185.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 1m39.919s sed -e 's/^/ # /;' fb.GCA_002082055.1.chainRBest.GCA_001949185.1.txt # 13053514 bases of 104154999 (12.533%) in intersection ##############################################################################