9393c53b555592fba153dd1608281eb68867bb89 lrnassar Wed Oct 9 11:32:59 2024 -0700 Two chains built for refs #34516 diff --git src/hg/makeDb/doc/asmHubs/lastzRuns.txt src/hg/makeDb/doc/asmHubs/lastzRuns.txt index 67d6d6e..e97b414 100644 --- src/hg/makeDb/doc/asmHubs/lastzRuns.txt +++ src/hg/makeDb/doc/asmHubs/lastzRuns.txt @@ -3112,15 +3112,180 @@ -target2bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \ GCF_019923935.1 GCF_029407905.1) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 91m43.292s sed -e 's/^/ # /;' fb.GCF_019923935.1.chainRBest.GCF_029407905.1.txt # 2597306727 bases of 2622460639 (99.041%) in intersection ############################################################################## real 1396m44.789s user 0m4.932s sys 0m5.466s + +############################################################################## +# LASTZ domestic cattle GCF_002263795.3 vs. Cow BosTau9 +# (DONE - 2024-10-03 - lrnassar) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzBosTau9.2024-10-03 + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzBosTau9.2024-10-03 + + printf '# Cow BosTau9 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: 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/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzBosTau9.2024-10-03 +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 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 1171m36.873s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainBosTau9Link.txt + # 2721933548 bases of 2770686120 (98.240%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynBosTau9Link.txt + # 2719316668 bases of 2770686120 (98.146%) 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" \ + \ + GCF_002263795.3 bosTau9) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 71m33.078s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.BosTau9.txt + # 2710500802 bases of 2770686120 (97.828%) in intersection + + ### and for the swap + + cd /hive/data/genomes/bosTau9/bed/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 /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzBosTau9.2024-10-03/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 511m22.768s + + sed -e 's/^/ # /;' fb.bosTau9.chainGCF_002263795.3Link.txt + # 2710592521 bases of 2715853792 (99.806%) in intersection + sed -e 's/^/ # /;' fb.bosTau9.chainSynGCF_002263795.3Link.txt + # 2710435411 bases of 2715853792 (99.800%) 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" \ + \ + bosTau9 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 74m39.910s + + sed -e 's/^/ # /;' fb.bosTau9.chainRBest.GCF_002263795.3.txt + # 2710500916 bases of 2715853792 (99.803%) in intersection + +############################################################################## + +# LASTZ domestic cattle GCF_002263795.3 vs. domestic cattle GCA_000003205.6 +# (DONE - 2024-10-07 - lrnassar) + + mkdir /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCA_000003205.6.2024-10-07 + cd /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCA_000003205.6.2024-10-07 + + printf '# domestic cattle GCA_000003205.6 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: domestic cattle 2015-11-19 GCA_000003205.6_Btau_5.0.1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/000/003/205/GCA_000003205.6/GCA_000003205.6.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/000/003/205/GCA_000003205.6/GCA_000003205.6.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/lastzGCA_000003205.6.2024-10-07 +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 GCA_000003205.6_Btau_5.0.1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 963m12.167s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainGCA_000003205.6Link.txt + # 2692604174 bases of 2770686120 (97.182%) in intersection + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainSynGCA_000003205.6Link.txt + # 2674440890 bases of 2770686120 (96.526%) 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/GCA/000/003/205/GCA_000003205.6/GCA_000003205.6.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/000/003/205/GCA_000003205.6/GCA_000003205.6.chrom.sizes.txt" \ + GCF_002263795.3 GCA_000003205.6) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 101m31.206s + + sed -e 's/^/ # /;' fb.GCF_002263795.3.chainRBest.GCA_000003205.6.txt + # 2635211813 bases of 2770686120 (95.110%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/000/003/205/GCA_000003205.6_Btau_5.0.1/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 GCA_000003205.6_Btau_5.0.1 /hive/data/genomes/asmHubs/allBuild/GCF/002/263/795/GCF_002263795.3_ARS-UCD2.0/trackData/lastzGCA_000003205.6.2024-10-07/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 725m22.800s + + sed -e 's/^/ # /;' fb.GCA_000003205.6.chainGCF_002263795.3Link.txt + # 2688308977 bases of 2724980740 (98.654%) in intersection + sed -e 's/^/ # /;' fb.GCA_000003205.6.chainSynGCF_002263795.3Link.txt + # 2663500489 bases of 2724980740 (97.744%) 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/GCA/000/003/205/GCA_000003205.6/GCA_000003205.6.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/000/003/205/GCA_000003205.6/GCA_000003205.6.chrom.sizes.txt" \ + GCA_000003205.6 GCF_002263795.3) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 115m10.092s + + sed -e 's/^/ # /;' fb.GCA_000003205.6.chainRBest.GCF_002263795.3.txt + # 2640372564 bases of 2724980740 (96.895%) in intersection + +##############################################################################