1ac19241d8c26d55fe304ed17a3cc41d2c3c5115 jnavarr5 Thu Sep 5 15:20:13 2024 -0700 Adding makedocs for liftOver files created, refs #34305 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index ff68beb..74f30b5 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -2788,16 +2788,98 @@ -targetSizes="/hive/data/genomes/asmHubs/GCF/001/704/415/GCF_001704415.2/GCF_001704415.2.chrom.sizes.txt" \ GCF_001704415.2 oviAri4) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 180m47.478s sed -e 's/^/ # /;' fb.GCF_001704415.2.chainRBest.OviAri4.txt # 2474132806 bases of 2922617086 (84.655%) in intersection ############################################################################## ### elapsed time: 45h 34m 01s Sun Jun 9 08:32:19 PDT 2024 ################################################################## +############################################################################## +# LASTZ domestic cattle GCF_002263795.3 vs. Bactrian camel GCF_000767855.1 +# (DONE - 2024-08-29 - jairo) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_000767855.1.2024-08-29 + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_000767855.1.2024-08-29 + + printf '# Bactrian camel GCF_000767855.1 vs. domestic cattle GCF_002263795.3 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: domestic cattle 2023-07-01 GCF_002263795.3_ARS-UCD2.0 +SEQ1_DIR=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit +SEQ1_LEN=/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: Bactrian camel 2014-10-23 GCF_000767855.1_Ca_bactrianus_MBC_1.0 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_000767855.1.2024-08-29 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -tAsmId GCF_002263795.3_ARS-UCD2.0 -qAsmId GCF_000767855.1_Ca_bactrianus_MBC_1.0 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 664m12.390s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainGCF_000767855.1Link.txt + # 1550318527 bases of 2770686120 (55.954%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynGCF_000767855.1Link.txt + # 1464637990 bases of 2770686120 (52.862%) in intersection + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -target2Bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.chrom.sizes.txt" \ + GCF_002263795.3 GCF_000767855.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 205m40.404s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.GCF_000767855.1.txt + # 1447494230 bases of 2770686120 (52.243%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/000/767/855/GCF_000767855.1_Ca_bactrianus_MBC_1.0/trackData/blastz.GCF_002263795.3.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -tAsmId GCF_002263795.3_ARS-UCD2.0 -qAsmId GCF_000767855.1_Ca_bactrianus_MBC_1.0 /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCF_000767855.1.2024-08-29/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 136m15.410s + + sed -e 's/^/ # /;' fb.GCF_000767855.1.chainGCF_002263795.3Link.txt + # 1531884279 bases of 1992663268 (76.876%) in intersection + sed -e 's/^/ # /;' fb.GCF_000767855.1.chainSynGCF_002263795.3Link.txt + # 1437058753 bases of 1992663268 (72.117%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + -query2bit="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/002/263/795/GCF_002263795.3/GCF_002263795.3.chrom.sizes.txt" \ + -target2bit="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCF/000/767/855/GCF_000767855.1/GCF_000767855.1.chrom.sizes.txt" \ + GCF_000767855.1 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 204m42.533s + + sed -e 's/^/ # /;' fb.GCF_000767855.1.chainRBest.GCF_002263795.3.txt + # 1444586026 bases of 1992663268 (72.495%) in intersection + +##############################################################################