089042f2c2941c58f286665e236311bddb6bed46 mspeir Wed Jun 26 08:40:58 2024 -0700 Adding lastz run with GCA_921999865.2, refs #33195 diff --git src/hg/makeDb/doc/mm39/lastzRuns.txt src/hg/makeDb/doc/mm39/lastzRuns.txt index 0cdab6a..0219aea 100644 --- src/hg/makeDb/doc/mm39/lastzRuns.txt +++ src/hg/makeDb/doc/mm39/lastzRuns.txt @@ -3494,15 +3494,414 @@ \ -target2bit="/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.2bit" \ -targetSizes="/hive/data/genomes/asmHubs/GCA/921/997/145/GCA_921997145.2/GCA_921997145.2.chrom.sizes.txt" \ GCA_921997145.2 mm39) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 63m16.206s sed -e 's/^/ # /;' fb.GCA_921997145.2.chainRBest.Mm39.txt # 2461542910 bases of 2519913072 (97.684%) in intersection real 2852m3.826s user 0m2.832s sys 0m2.990s ############################################################################## + +# LASTZ Mouse Mm39 vs. house mouse GCA_921999865.2 +# (DONE - 2024-06-24 - mspeir) + + mkdir /hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24 + cd /hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24 + + printf '# house mouse GCA_921999865.2 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: house mouse 2022-07-01 GCA_921999865.2_C57BL_6NJ_v3 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_921999865.2_C57BL_6NJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 836m4.496s + + sed -e 's/^/ # /;' fb.mm39.chainGCA_921999865.2Link.txt + # 2617230462 bases of 2728222451 (95.932%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCA_921999865.2Link.txt + # 2559197304 bases of 2728222451 (93.805%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt" \ + mm39 GCA_921999865.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 94m40.087s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_921999865.2.txt + # 2496889698 bases of 2728222451 (91.521%) in intersection + + ### and for the swap +# swap into: /hive/data/genomes/asmHubs/allBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/blastz.mm39.swap +# running /hive/data/genomes/asmHubs/allBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/blastz.mm39.swap/runSwap.sh ++ cd /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3 ++ export defaultName=GCA_921999865.2_C57BL_6NJ_v3 ++ defaultName=GCA_921999865.2_C57BL_6NJ_v3 ++ export asmId=GCA_921999865.2_C57BL_6NJ_v3 ++ asmId=GCA_921999865.2_C57BL_6NJ_v3 ++ export buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3 ++ buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3 ++ rm -f GCA_921999865.2_C57BL_6NJ_v3.chromAlias.txt ++ ln -s trackData/chromAlias/GCA_921999865.2_C57BL_6NJ_v3.chromAlias.txt . ++ '[' -s trackData/chromAlias/GCA_921999865.2_C57BL_6NJ_v3.chromAlias.bb ']' ++ rm -f GCA_921999865.2_C57BL_6NJ_v3.chromAlias.bb ++ ln -s trackData/chromAlias/GCA_921999865.2_C57BL_6NJ_v3.chromAlias.bb . ++ /cluster/home/mspeir/kent/src/hg/utils/automation/asmHubTrackDb.sh GCA_921999865.2_C57BL_6NJ_v3 GCA_921999865.2_C57BL_6NJ_v3 /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3 +# no ensGene found +single chainNet ++ '[' 2 -ne 2 ']' ++ export asmId=GCA_921999865.2_C57BL_6NJ_v3 ++ asmId=GCA_921999865.2_C57BL_6NJ_v3 ++ export buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3 ++ buildDir=/hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3 ++ export hubLinks=/hive/data/genomes/asmHubs/hubLinks ++ hubLinks=/hive/data/genomes/asmHubs/hubLinks ++ export accessionId=GCA_921999865.2_C57BL_6NJ_v3 ++ accessionId=GCA_921999865.2_C57BL_6NJ_v3 ++ case ${asmId} in +++ echo GCA_921999865.2_C57BL_6NJ_v3 +++ awk -F_ '{printf "%s_%s", $1, $2}' ++ accessionId=GCA_921999865.2 ++ export scriptDir=/cluster/home/mspeir/kent/src/hg/utils/automation ++ scriptDir=/cluster/home/mspeir/kent/src/hg/utils/automation ++ mkdir -p /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi ++ mkdir -p /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/liftOver ++ export chainNetPriority=1 ++ chainNetPriority=1 ++ printf '# asmHubChainNetTrackDb.pl GCA_921999865.2_C57BL_6NJ_v3 /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3\n' +# asmHubChainNetTrackDb.pl GCA_921999865.2_C57BL_6NJ_v3 /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3 ++ for D in '${buildDir}/trackData/lastz.*' ++ targetDb=GCA_921999865.2 +++ basename /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39 ++ lastzDir=lastz.mm39 +++ echo lastz.mm39 +++ sed -e 's/lastz.//;' ++ otherDb=mm39 ++ OtherDb=Mm39 +++ ls -d /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/download/GCA_921999865.2_C57BL_6NJ_v3_assembly_report.txt ++ asmReport=/hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/download/GCA_921999865.2_C57BL_6NJ_v3_assembly_report.txt ++ overChain=GCA_921999865.2.mm39.over.chain.gz ++ overToChain=GCA_921999865.2ToMm39.over.chain.gz ++ printf 'asmReport: %s\n' /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/download/GCA_921999865.2_C57BL_6NJ_v3_assembly_report.txt +asmReport: /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/download/GCA_921999865.2_C57BL_6NJ_v3_assembly_report.txt ++ '[' '!' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/download/GCA_921999865.2_C57BL_6NJ_v3_assembly_report.txt ']' ++ '[' '!' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/chainMm39.bb ']' ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39Link.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39Link.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39Link.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39Link.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.summary.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.summary.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.summary.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.liftOverNet.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.liftOverNet.summary.bb ++ rm -f /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/liftOver/GCA_921999865.2ToMm39.over.chain.gz ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/GCA_921999865.2.mm39.over.chain.gz ']' ++ ln -s ../trackData/lastz.mm39/axtChain/GCA_921999865.2.mm39.over.chain.gz /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/liftOver/GCA_921999865.2ToMm39.over.chain.gz ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/chainMm39.bb ']' ++ ln -s ../trackData/lastz.mm39/axtChain/chainMm39.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39.bb ++ ln -s ../trackData/lastz.mm39/axtChain/chainMm39Link.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39Link.bb ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.net.bb ']' ++ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.net.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.bb ++ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.net.summary.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.summary.bb ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/chainSynMm39.bb ']' ++ ln -s ../trackData/lastz.mm39/axtChain/chainSynMm39.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39.bb ++ ln -s ../trackData/lastz.mm39/axtChain/chainSynMm39Link.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39Link.bb ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.synNet.bb ']' ++ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.synNet.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.bb ++ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.synNet.summary.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.summary.bb ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/chainRBestMm39.bb ']' ++ ln -s ../trackData/lastz.mm39/axtChain/chainRBestMm39.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39.bb ++ ln -s ../trackData/lastz.mm39/axtChain/chainRBestMm39Link.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39Link.bb ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.rbestNet.bb ']' ++ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.rbestNet.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.bb ++ ln -s ../trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.rbestNet.summary.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.summary.bb ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/axtChain/chainLiftOverMm39.bb ']' ++ printf '# making chainLiftOverMm39.bb\n' +# making chainLiftOverMm39.bb ++ ln -s ../trackData/lastz.mm39/axtChain/chainLiftOverMm39.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39.bb ++ ln -s ../trackData/lastz.mm39/axtChain/chainLiftOverMm39Link.bb /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39Link.bb ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/lastz.mm39/bigMaf/GCA_921999865.2.mm39.liftOverNet.bb ']' +++ echo mm39 +++ cut -c1-2 ++ otherPrefix=mm ++ '[' mm = GC ']' +++ hgsql -N -e 'select organism from dbDb where name="mm39"' hgcentraltest ++ organism=Mouse +++ hgsql -N -e 'select scientificName from dbDb where name="mm39"' hgcentraltest ++ sciName='Mus musculus' +++ hgsql -N -e 'select taxId from dbDb where name="mm39"' hgcentraltest ++ taxId=10090 +++ hgsql -N -e 'select description from dbDb where name="mm39"' hgcentraltest ++ o_date='Jun. 2020 (GRCm39/mm39)' +++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl mm39 GCA_921999865.2 +++ grep matrix ++ matrix='matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91' +++ echo mm39 +++ cut -c1-2 ++ otherPrefix=mm ++ '[' mm = GC ']' +++ hgsql -N -e 'select organism from dbDb where name="mm39"' hgcentraltest ++ organism=Mouse +++ hgsql -N -e 'select scientificName from dbDb where name="mm39"' hgcentraltest ++ sciName='Mus musculus' +++ hgsql -N -e 'select taxId from dbDb where name="mm39"' hgcentraltest ++ taxId=10090 +++ hgsql -N -e 'select description from dbDb where name="mm39"' hgcentraltest ++ o_date='Jun. 2020 (GRCm39/mm39)' +++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl mm39 GCA_921999865.2 +++ grep matrix ++ matrix='matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91' +++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl mm39 GCA_921999865.2 +++ grep MinScore ++ minScore='chainMinScore 3000' +++ grep LinearGap +++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl mm39 GCA_921999865.2 ++ linGap='chainLinearGap medium' ++ printf '############################################################################## +# mm39 - Mouse - Mus musculus - taxId: 10090 +############################################################################## +' ++ printf 'track chainNetMm39 +compositeTrack on +shortLabel Mouse Chain/Net +longLabel Mouse (Jun. 2020 (GRCm39/mm39)), Chain and Net Alignments +subGroup1 view Views chain=Chain net=Net +dragAndDrop subTracks +visibility hide +group compGeno +' ++ printf 'priority 100.1 +color 0,0,0 +altColor 100,50,0 +type bed 3 +sortOrder view=+ +' ++ '[' 'xmatrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91y' = xy ']' ++ printf 'matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 +chainMinScore 3000 +chainLinearGap medium +matrixHeader A, C, G, T +otherDb mm39 +html html/GCA_921999865.2_C57BL_6NJ_v3.chainNet + +' ++ printf ' track chainNetMm39Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetMm39 + spectrum on + + track chainMm39 + parent chainNetMm39Viewchain + subGroups view=chain + shortLabel Mouse Chain + longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Chained Alignments + type bigChain mm39 + bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39.bb + linkDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainMm39Link.bb + priority %d + +' 1 ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39.bb ']' ++ printf ' track chainSynMm39 + parent chainNetMm39Viewchain + subGroups view=chain + shortLabel Mouse synChain + longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Syntenic Chained Alignments + type bigChain mm39 + bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39.bb + linkDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainSynMm39Link.bb + priority %d + +' 2 ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39.bb ']' ++ printf ' track chainRBestMm39 + parent chainNetMm39Viewchain + subGroups view=chain + shortLabel Mouse rbChain + longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Reciprocal Best Chained Alignments + type bigChain mm39 + bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39.bb + linkDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainRBestMm39Link.bb + priority %d + +' 3 ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39.bb ']' ++ printf ' track chainLiftOverMm39 + parent chainNetMm39Viewchain + subGroups view=chain + shortLabel Mouse loChain + longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Lift Over Chained Alignments + type bigChain mm39 + bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39.bb + linkDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.chainLiftOverMm39Link.bb + priority %d + +' 4 ++ printf ' track mafNetMm39Viewnet + shortLabel Net + view net + visibility full + parent chainNetMm39 + + track netMm39 + parent mafNetMm39Viewnet + subGroups view=net + shortLabel Mouse net + longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Net Alignment + type bigMaf + bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.bb + summary bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.net.summary.bb + speciesOrder mm39 + priority %d + +' 5 ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.summary.bb ']' ++ printf ' track synNetMm39 + parent mafNetMm39Viewnet + subGroups view=net + shortLabel Mouse synNet + longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Syntenic Net Alignment + type bigMaf + bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.bb + summary bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.synNet.summary.bb + speciesOrder mm39 + priority %d + +' 6 ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.summary.bb ']' ++ printf ' track rbestNetMm39 + parent mafNetMm39Viewnet + subGroups view=net + shortLabel Mouse rbestNet + longLabel Mouse (Jun. 2020 (GRCm39/mm39)) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.bb + summary bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.rbestNet.summary.bb + speciesOrder mm39 + priority %d + +' 7 ++ '[' -s /hive/data/genomes/asmHubs/genbankBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/bbi/GCA_921999865.2_C57BL_6NJ_v3.mm39.liftOverNet.summary.bb ']' + +############################################################################## +# LASTZ Mouse Mm39 vs. house mouse GCA_921999865.2 +# (DONE - 2024-06-24 - mspeir) + + mkdir /hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24 + cd /hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24 + + printf '# house mouse GCA_921999865.2 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: house mouse 2022-07-01 GCA_921999865.2_C57BL_6NJ_v3 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCA_921999865.2_C57BL_6NJ_v3 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 836m4.496s + + sed -e 's/^/ # /;' fb.mm39.chainGCA_921999865.2Link.txt + # 2617230462 bases of 2728222451 (95.932%) in intersection + sed -e 's/^/ # /;' fb.mm39.chainSynGCA_921999865.2Link.txt + # 2559197304 bases of 2728222451 (93.805%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt" \ + mm39 GCA_921999865.2) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 94m40.087s + + sed -e 's/^/ # /;' fb.mm39.chainRBest.GCA_921999865.2.txt + # 2496889698 bases of 2728222451 (91.521%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCA/921/999/865/GCA_921999865.2_C57BL_6NJ_v3/trackData/blastz.mm39.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCA_921999865.2_C57BL_6NJ_v3 /hive/data/genomes/mm39/bed/lastzGCA_921999865.2.2024-06-24/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 320m49.857s + + sed -e 's/^/ # /;' fb.GCA_921999865.2.chainMm39Link.txt + # 2503336620 bases of 2514593528 (99.552%) in intersection + sed -e 's/^/ # /;' fb.GCA_921999865.2.chainSynMm39Link.txt + # 2500544042 bases of 2514593528 (99.441%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -target2bit="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.2bit" \ +-targetSizes="/hive/data/genomes/asmHubs/GCA/921/999/865/GCA_921999865.2/GCA_921999865.2.chrom.sizes.txt" \ + GCA_921999865.2 mm39) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 67m13.662s + + sed -e 's/^/ # /;' fb.GCA_921999865.2.chainRBest.Mm39.txt + # 2497498017 bases of 2514593528 (99.320%) in intersection + +real 1318m52.288s +user 0m2.240s +sys 0m2.560s + +##############################################################################