7026265ab12f9aa4715453d5c84cdb703d2f4220 gperez2 Mon Mar 21 16:30:12 2022 -0700 water buffalo GCF_003121395.1 vs. Cow BosTau9 lastz/chain/net run for user, refs #29082 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 2d08c55..8f0c3e7 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -1685,15 +1685,105 @@ -target2bit="/hive/data/genomes/asmHubs/GCF/000/002/845/GCF_000002845.2/GCF_000002845.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/000/002/845/GCF_000002845.2/GCF_000002845.2.chrom.sizes.txt" \ GCF_000002845.2 GCA_000340355.2) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 1m2.112s sed -e 's/^/ # /;' fb.GCF_000002845.2.chainRBest.GCA_000340355.2.txt # 30310385 bases of 32068771 (94.517%) in intersection ############################################################################## real 27m14.153s user 0m1.233s sys 0m1.147s +############################################################################# +# LASTZ water buffalo GCF_003121395.1 vs. Cow BosTau9 (DONE - 2022-01-17) + + ./pairLastz.sh GCF_003121395.1_ASM312139v1 bosTau9 mammal mammal + + # this command outputs this makeDoc text: + + cat /hive/data/genomes/asmHubs/refseqBuild/GCF/003/121/395/GCF_003121395.1_ASM312139v1/trackData/lastzBosTau9.2022-03-15/makeDoc.txt + +############################################################################## +# LASTZ water buffalo GCF_003121395.1 vs. Cow BosTau9 +# (DONE - 2022-03-21 - hiram) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/003/121/395/GCF_003121395.1_ASM312139v1/trackData/lastzBosTau9.2022-03-15 + cd /hive/data/genomes/asmHubs/allBuild/GCF/003/121/395/GCF_003121395.1_ASM312139v1/trackData/lastzBosTau9.2022-03-15 + + printf '# Cow BosTau9 vs. water buffalo GCF_003121395.1 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: water buffalo GCF_003121395.1 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Cow BosTau9 +SEQ2_DIR=/hive/data/genomes/bosTau9/bosTau9.2bit +SEQ2_LEN=/hive/data/genomes/bosTau9/chrom.sizes +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/003/121/395/GCF_003121395.1_ASM312139v1/trackData/lastzBosTau9.2022-03-15 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_003121395.1_ASM312139v1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 586m13.240s + + sed -e 's/^/ # /;' fb.GCF_003121395.1.chainBosTau9Link.txt + # 2530022888 bases of 2655780776 (95.265%) in intersection + sed -e 's/^/ # /;' fb.GCF_003121395.1.chainSynBosTau9Link.txt + # 2503488174 bases of 2655780776 (94.266%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.chrom.sizes.txt" \ + \ + GCF_003121395.1 bosTau9) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 131m51.569s + + sed -e 's/^/ # /;' fb.GCF_003121395.1.chainRBest.BosTau9.txt + # 2481923005 bases of 2655780776 (93.454%) in intersection + + ### and for the swap + + cd /hive/data/genomes/bosTau9/bed/blastz.GCF_003121395.1.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_003121395.1_ASM312139v1 /hive/data/genomes/asmHubs/allBuild/GCF/003/121/395/GCF_003121395.1_ASM312139v1/trackData/lastzBosTau9.2022-03-15/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 217m58.432s + + sed -e 's/^/ # /;' fb.bosTau9.chainGCF_003121395.1Link.txt + # 2545585532 bases of 2715853792 (93.731%) in intersection + sed -e 's/^/ # /;' fb.bosTau9.chainSynGCF_003121395.1Link.txt + # 2515328392 bases of 2715853792 (92.616%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/003/121/395/GCF_003121395.1/GCF_003121395.1.chrom.sizes.txt" \ + \ + bosTau9 GCF_003121395.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 142m40.163s + + sed -e 's/^/ # /;' fb.bosTau9.chainRBest.GCF_003121395.1.txt + # 2481700410 bases of 2715853792 (91.378%) in intersection + +##############################################################################