6428d3411111567658e7496a9d131dcbe85034f6 hiram Tue Jul 19 11:36:26 2022 -0700 platypus to platypus per user request refs #29753 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index fe3a88b..f0309d2 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -1869,15 +1869,94 @@ # 2466586935 bases of 3050398082 (80.861%) in intersection \ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ -query2bit="/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.2bit" \ -querySizes="/hive/data/genomes/asmHubs/GCF/012/559/485/GCF_012559485.2/GCF_012559485.2.chrom.sizes.txt" \ -target2bit="/hive/data/genomes/asmHubs/GCF/002/880/755/GCF_002880755.1/GCF_002880755.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/002/880/755/GCF_002880755.1/GCF_002880755.1.chrom.sizes.txt" \ GCF_002880755.1 GCF_012559485.2) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 146m55.957s sed -e 's/^/ # /;' fb.GCF_002880755.1.chainRBest.GCF_012559485.2.txt # 2408485685 bases of 3050398082 (78.956%) in intersection ############################################################################## +# LASTZ platypus GCF_004115215.2 vs. platypus GCA_002966995.1 +# (DONE - 2022-07-18 - hiram) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/004/115/215/GCF_004115215.2_mOrnAna1.pri.v4/trackData/lastzGCA_002966995.1.2022-07-14 + cd /hive/data/genomes/asmHubs/allBuild/GCF/004/115/215/GCF_004115215.2_mOrnAna1.pri.v4/trackData/lastzGCA_002966995.1.2022-07-14 + + printf '# platypus GCA_002966995.1 vs. platypus GCF_004115215.2 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: platypus 2020-11-06 GCF_004115215.2_mOrnAna1.pri.v4 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: platypus 2018-03-02 GCA_002966995.1_ASM296699v1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/004/115/215/GCF_004115215.2_mOrnAna1.pri.v4/trackData/lastzGCA_002966995.1.2022-07-14 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_004115215.2_mOrnAna1.pri.v4 -qAsmId GCA_002966995.1_ASM296699v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + + sed -e 's/^/ # /;' fb.GCF_004115215.2.chainGCA_002966995.1Link.txt + # 1833760395 bases of 1859281927 (98.627%) in intersection + sed -e 's/^/ # /;' fb.GCF_004115215.2.chainSynGCA_002966995.1Link.txt + # 1822260569 bases of 1859281927 (98.009%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.chrom.sizes.txt" \ + GCF_004115215.2 GCA_002966995.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + + sed -e 's/^/ # /;' fb.GCF_004115215.2.chainRBest.GCA_002966995.1.txt + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/002/966/995/GCA_002966995.1_ASM296699v1/trackData/blastz.GCF_004115215.2.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_004115215.2_mOrnAna1.pri.v4 -qAsmId GCA_002966995.1_ASM296699v1 /hive/data/genomes/asmHubs/allBuild/GCF/004/115/215/GCF_004115215.2_mOrnAna1.pri.v4/trackData/lastzGCA_002966995.1.2022-07-14/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 505m1.293s + + sed -e 's/^/ # /;' fb.GCA_002966995.1.chainGCF_004115215.2Link.txt + # 1968124670 bases of 1990409179 (98.880%) in intersection + sed -e 's/^/ # /;' fb.GCA_002966995.1.chainSynGCF_004115215.2Link.txt + # 1943307833 bases of 1990409179 (97.634%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/004/115/215/GCF_004115215.2/GCF_004115215.2.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/002/966/995/GCA_002966995.1/GCA_002966995.1.chrom.sizes.txt" \ + GCA_002966995.1 GCF_004115215.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 44m40.845s + + sed -e 's/^/ # /;' fb.GCA_002966995.1.chainRBest.GCF_004115215.2.txt + # 1816571806 bases of 1990409179 (91.266%) in intersection + +##############################################################################