408f7dd97515881a86b62c29955b2ca17926e9bc gperez2 Tue Dec 6 20:58:44 2022 -0800 mm 9 v GCA_004027735.1 lastz/chain/net run for user, refs #30097 diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt index 82a5dbc..14184eb 100644 --- src/hg/makeDb/doc/mm39/lastzRuns.txt +++ src/hg/makeDb/doc/mm39/lastzRuns.txt @@ -2307,15 +2307,106 @@ sed -e 's/^/ # /;' fb.hg19.chainMm39Link.txt # 969322683 bases of 2991710746 (32.400%) in intersection sed -e 's/^/ # /;' fb.hg19.chainSynMm39Link.txt # 921405754 bases of 2991710746 (30.799%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ hg19 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 299m2.449s sed -e 's/^/ # /;' fb.hg19.chainRBest.Mm39.txt # 892863094 bases of 2991710746 (29.845%) in intersection ############################################################################## +# LASTZ Mouse Mm39 vs. Seba's short-tailed bat GCA_004027735.1 (DONE - 2022-10-10 - 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 \ + mm39 GCA_004027735.1_CarPer_v1_BIUU mammal mammal) \ + > mm39.GCA_004027735.1_20221010.log 2>&1 & + # check the total time +grep -w real mm39.GCA_004027735.1_20221010.log | tail -1 | sed -e 's/^/ # /;' + # real 4941m5.588s +############################################################################## +# LASTZ Mouse Mm39 vs. Seba's short-tailed bat GCA_004027735.1 +# (DONE - 2022-10-10 - Gerardo) + + mkdir /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10 + cd /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10 + + printf '# Seba's short-tailed bat GCA_004027735.1 vs. Mouse Mm39 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Mouse mm39 +SEQ1_DIR=/hive/data/genomes/mm39/mm39.2bit +SEQ1_LEN=/hive/data/genomes/mm39/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Seba's short-tailed bat 2019-01-16 GCA_004027735.1_CarPer_v1_BIUU +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=500 + +BASE=/hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_004027735.1_CarPer_v1_BIUU -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 682m7.456s + + sed -e 's/^/ # /;' fb.mm39.chainGCA_004027735.1Link.txt + # 646007750 bases of 2728222451 (23.679%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCA_004027735.1Link.txt + # 266104069 bases of 2728222451 (9.754%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.chrom.sizes.txt" \ + mm39 GCA_004027735.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 514m58.090s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_004027735.1.txt + # 613273332 bases of 2728222451 (22.479%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/004/027/735/GCA_004027735.1_CarPer_v1_BIUU/trackData/blastz.mm39.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_004027735.1_CarPer_v1_BIUU /hive/data/genomes/mm39/bed/lastzGCA_004027735.1.2022-10-10/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 1925m11.716s + + sed -e 's/^/ # /;' fb.GCA_004027735.1.chainMm39Link.txt + # 687442098 bases of 2689411905 (25.561%) in intersection + sed -e 's/^/ # /;' fb.GCA_004027735.1.chainSynMm39Link.txt + # 261303649 bases of 2689411905 (9.716%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/004/027/735/GCA_004027735.1/GCA_004027735.1.chrom.sizes.txt" \ + GCA_004027735.1 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 1818m46.969s + + sed -e 's/^/ # /;' fb.GCA_004027735.1.chainRBest.Mm39.txt + # 614276787 bases of 2689411905 (22.841%) in intersection +