c139f35504866c1dcf0eec5e3e07a83da8866fe5 mspeir Tue Jan 16 19:49:03 2024 -0800 adding makedocs for various lastz runs for liftOver files in MLQ request, refs #32804 diff --git src/hg/makeDb/doc/hg38/lastzRuns.txt src/hg/makeDb/doc/hg38/lastzRuns.txt index 74f9b92..9fef38d 100644 --- src/hg/makeDb/doc/hg38/lastzRuns.txt +++ src/hg/makeDb/doc/hg38/lastzRuns.txt @@ -13895,15 +13895,398 @@ sed -e 's/^/ # /;' fb.hs1.chainHg38Link.txt # 2906145588 bases of 3117292070 (93.227%) in intersection sed -e 's/^/ # /;' fb.hs1.chainSynHg38Link.txt # 2896674405 bases of 3117292070 (92.923%) in intersection time (~/kent/src/hg/utils/automation/doRecipBest.pl -load -workhorse=hgwdev -buildDir=`pwd` \ hs1 hg38) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' # real 88m35.809s sed -e 's/^/ # /;' fb.hs1.chainRBest.Hg38.txt # 2863655887 bases of 3117292070 (91.864%) in intersection ############################################################################## +# LASTZ Human Hg38 vs. water buffalo GCF_019923935.1 +# (DONE - 2023-12-30 - mspeir) + + mkdir /hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30 + cd /hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30 + + printf '# water buffalo GCF_019923935.1 vs. Human Hg38 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Human hg38 +SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit +SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_019923935.1_NDDB_SH_1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 931m33.045s + + sed -e 's/^/ # /;' fb.hg38.chainGCF_019923935.1Link.txt + # 1441231401 bases of 3299210039 (43.684%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCF_019923935.1Link.txt + # 1373195820 bases of 3299210039 (41.622%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \ + hg38 GCF_019923935.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 329m20.127s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCF_019923935.1.txt + # 1288371538 bases of 3299210039 (39.051%) in intersection + + ### and for the swap +# swap into: /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.hg38.swap +# running /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.hg38.swap/runSwap.sh ++ cd /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 ++ export defaultName=GCF_019923935.1_NDDB_SH_1 ++ defaultName=GCF_019923935.1_NDDB_SH_1 ++ export asmId=GCF_019923935.1_NDDB_SH_1 ++ asmId=GCF_019923935.1_NDDB_SH_1 ++ export buildDir=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 ++ buildDir=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 ++ rm -f GCF_019923935.1_NDDB_SH_1.chromAlias.txt ++ ln -s trackData/chromAlias/GCF_019923935.1_NDDB_SH_1.chromAlias.txt . ++ '[' -s trackData/chromAlias/GCF_019923935.1_NDDB_SH_1.chromAlias.bb ']' ++ rm -f GCF_019923935.1_NDDB_SH_1.chromAlias.bb ++ ln -s trackData/chromAlias/GCF_019923935.1_NDDB_SH_1.chromAlias.bb . ++ /cluster/home/mspeir/kent/src/hg/utils/automation/asmHubTrackDb.sh GCF_019923935.1_NDDB_SH_1 GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 +# no ensGene found +single chainNet ++ '[' 2 -ne 2 ']' ++ export asmId=GCF_019923935.1_NDDB_SH_1 ++ asmId=GCF_019923935.1_NDDB_SH_1 ++ export buildDir=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 ++ buildDir=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 ++ export hubLinks=/hive/data/genomes/asmHubs/hubLinks ++ hubLinks=/hive/data/genomes/asmHubs/hubLinks ++ export accessionId=GCF_019923935.1_NDDB_SH_1 ++ accessionId=GCF_019923935.1_NDDB_SH_1 ++ case ${asmId} in +++ echo GCF_019923935.1_NDDB_SH_1 +++ awk -F_ '{printf "%s_%s", $1, $2}' ++ accessionId=GCF_019923935.1 ++ export scriptDir=/cluster/home/mspeir/kent/src/hg/utils/automation ++ scriptDir=/cluster/home/mspeir/kent/src/hg/utils/automation ++ mkdir -p /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi ++ mkdir -p /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/liftOver ++ export chainNetPriority=1 ++ chainNetPriority=1 ++ printf '# asmHubChainNetTrackDb.pl GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1\n' +# asmHubChainNetTrackDb.pl GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1 ++ for D in '${buildDir}/trackData/lastz.*' ++ targetDb=GCF_019923935.1 +++ basename /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38 ++ lastzDir=lastz.hg38 +++ echo lastz.hg38 +++ sed -e 's/lastz.//;' ++ otherDb=hg38 ++ OtherDb=Hg38 +++ ls -d /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/download/GCF_019923935.1_NDDB_SH_1_assembly_report.txt ++ asmReport=/hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/download/GCF_019923935.1_NDDB_SH_1_assembly_report.txt ++ overChain=GCF_019923935.1.hg38.over.chain.gz ++ overToChain=GCF_019923935.1ToHg38.over.chain.gz ++ printf 'asmReport: %s\n' /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/download/GCF_019923935.1_NDDB_SH_1_assembly_report.txt +asmReport: /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/download/GCF_019923935.1_NDDB_SH_1_assembly_report.txt ++ '[' '!' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/download/GCF_019923935.1_NDDB_SH_1_assembly_report.txt ']' ++ '[' '!' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/chainHg38.bb ']' ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainHg38.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainHg38Link.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38Link.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38Link.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainLiftOverHg38.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainLiftOverHg38Link.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.summary.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.summary.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.summary.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.liftOverNet.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.liftOverNet.summary.bb ++ rm -f /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/liftOver/GCF_019923935.1ToHg38.over.chain.gz ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/GCF_019923935.1.hg38.over.chain.gz ']' ++ ln -s ../trackData/lastz.hg38/axtChain/GCF_019923935.1.hg38.over.chain.gz /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/liftOver/GCF_019923935.1ToHg38.over.chain.gz ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/chainHg38.bb ']' ++ ln -s ../trackData/lastz.hg38/axtChain/chainHg38.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainHg38.bb ++ ln -s ../trackData/lastz.hg38/axtChain/chainHg38Link.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainHg38Link.bb ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.net.bb ']' ++ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.net.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.bb ++ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.net.summary.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.summary.bb ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/chainSynHg38.bb ']' ++ ln -s ../trackData/lastz.hg38/axtChain/chainSynHg38.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38.bb ++ ln -s ../trackData/lastz.hg38/axtChain/chainSynHg38Link.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38Link.bb ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.synNet.bb ']' ++ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.synNet.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.bb ++ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.synNet.summary.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.summary.bb ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/chainRBestHg38.bb ']' ++ ln -s ../trackData/lastz.hg38/axtChain/chainRBestHg38.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38.bb ++ ln -s ../trackData/lastz.hg38/axtChain/chainRBestHg38Link.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38Link.bb ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.rbestNet.bb ']' ++ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.rbestNet.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.bb ++ ln -s ../trackData/lastz.hg38/bigMaf/GCF_019923935.1.hg38.rbestNet.summary.bb /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.summary.bb ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/lastz.hg38/axtChain/chainLiftOverHg38.bb ']' ++ printf '# there is NO chainLiftOverHg38.bb\n' +# there is NO chainLiftOverHg38.bb +++ cut -c1-2 +++ echo hg38 ++ otherPrefix=hg ++ '[' hg = GC ']' +++ hgsql -N -e 'select organism from dbDb where name="hg38"' hgcentraltest ++ organism=Human +++ hgsql -N -e 'select scientificName from dbDb where name="hg38"' hgcentraltest ++ sciName='Homo sapiens' +++ hgsql -N -e 'select taxId from dbDb where name="hg38"' hgcentraltest ++ taxId=9606 +++ hgsql -N -e 'select description from dbDb where name="hg38"' hgcentraltest ++ o_date='Dec. 2013 (GRCh38/hg38)' +++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl hg38 GCF_019923935.1 +++ grep matrix ++ matrix='matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91' +++ echo hg38 +++ cut -c1-2 ++ otherPrefix=hg ++ '[' hg = GC ']' +++ hgsql -N -e 'select organism from dbDb where name="hg38"' hgcentraltest ++ organism=Human +++ hgsql -N -e 'select scientificName from dbDb where name="hg38"' hgcentraltest ++ sciName='Homo sapiens' +++ hgsql -N -e 'select taxId from dbDb where name="hg38"' hgcentraltest ++ taxId=9606 +++ hgsql -N -e 'select description from dbDb where name="hg38"' hgcentraltest ++ o_date='Dec. 2013 (GRCh38/hg38)' +++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl hg38 GCF_019923935.1 +++ 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 hg38 GCF_019923935.1 +++ grep MinScore ++ minScore='chainMinScore 3000' +++ /cluster/home/mspeir/kent/src/hg/utils/phyloTrees/findScores.pl hg38 GCF_019923935.1 +++ grep LinearGap ++ linGap='chainLinearGap medium' ++ printf '############################################################################## +# hg38 - Human - Homo sapiens - taxId: 9606 +############################################################################## +' ++ printf 'track chainNetHg38 +compositeTrack on +shortLabel Human Chain/Net +longLabel Human (Dec. 2013 (GRCh38/hg38)), 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 hg38 +html html/GCF_019923935.1_NDDB_SH_1.chainNet + +' ++ printf ' track chainNetHg38Viewchain + shortLabel Chain + view chain + visibility pack + parent chainNetHg38 + spectrum on + + track chainHg38 + parent chainNetHg38Viewchain + subGroups view=chain + shortLabel Human Chain + longLabel Human (Dec. 2013 (GRCh38/hg38)) Chained Alignments + type bigChain hg38 + bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainHg38.bb + linkDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainHg38Link.bb + priority %d + +' 1 ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38.bb ']' ++ printf ' track chainSynHg38 + parent chainNetHg38Viewchain + subGroups view=chain + shortLabel Human synChain + longLabel Human (Dec. 2013 (GRCh38/hg38)) Syntenic Chained Alignments + type bigChain hg38 + bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38.bb + linkDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainSynHg38Link.bb + priority %d + +' 2 ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38.bb ']' ++ printf ' track chainRBestHg38 + parent chainNetHg38Viewchain + subGroups view=chain + shortLabel Human rbChain + longLabel Human (Dec. 2013 (GRCh38/hg38)) Reciprocal Best Chained Alignments + type bigChain hg38 + bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38.bb + linkDataUrl bbi/GCF_019923935.1_NDDB_SH_1.chainRBestHg38Link.bb + priority %d + +' 3 ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.chainLiftOverHg38.bb ']' ++ printf ' track mafNetHg38Viewnet + shortLabel Net + view net + visibility full + parent chainNetHg38 + + track netHg38 + parent mafNetHg38Viewnet + subGroups view=net + shortLabel Human net + longLabel Human (Dec. 2013 (GRCh38/hg38)) Net Alignment + type bigMaf + bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.bb + summary bbi/GCF_019923935.1_NDDB_SH_1.hg38.net.summary.bb + speciesOrder hg38 + priority %d + +' 4 ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.summary.bb ']' ++ printf ' track synNetHg38 + parent mafNetHg38Viewnet + subGroups view=net + shortLabel Human synNet + longLabel Human (Dec. 2013 (GRCh38/hg38)) Syntenic Net Alignment + type bigMaf + bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.bb + summary bbi/GCF_019923935.1_NDDB_SH_1.hg38.synNet.summary.bb + speciesOrder hg38 + priority %d + +' 5 ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.summary.bb ']' ++ printf ' track rbestNetHg38 + parent mafNetHg38Viewnet + subGroups view=net + shortLabel Human rbestNet + longLabel Human (Dec. 2013 (GRCh38/hg38)) Reciprocal Best Net Alignment + type bigMaf + bigDataUrl bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.bb + summary bbi/GCF_019923935.1_NDDB_SH_1.hg38.rbestNet.summary.bb + speciesOrder hg38 + priority %d + +' 6 ++ '[' -s /hive/data/genomes/asmHubs/refseqBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/bbi/GCF_019923935.1_NDDB_SH_1.hg38.liftOverNet.summary.bb ']' +############################################################################## +# LASTZ Human Hg38 vs. water buffalo GCF_019923935.1 +# (DONE - 2023-12-30 - mspeir) + + mkdir /hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30 + cd /hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30 + + printf '# water buffalo GCF_019923935.1 vs. Human Hg38 +BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz + +# TARGET: Human hg38 +SEQ1_DIR=/hive/data/genomes/hg38/hg38.2bit +SEQ1_LEN=/hive/data/genomes/hg38/chrom.sizes +SEQ1_CHUNK=20000000 +SEQ1_LAP=10000 +SEQ1_LIMIT=40 + +# QUERY: water buffalo 2021-09-10 GCF_019923935.1_NDDB_SH_1 +SEQ2_DIR=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit +SEQ2_LEN=/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt +SEQ2_CHUNK=20000000 +SEQ2_LAP=0 +SEQ2_LIMIT=100 + +BASE=/hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30 +TMPDIR=/dev/shm + +' > DEF + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -verbose=2 `pwd`/DEF -syntenicNet \ + -qAsmId GCF_019923935.1_NDDB_SH_1 -workhorse=hgwdev -smallClusterHub=hgwdev -bigClusterHub=ku \ + -chainMinScore=3000 -chainLinearGap=medium) > do.log 2>&1 + grep -w real do.log | sed -e 's/^/ # /;' + # real 931m33.045s + + sed -e 's/^/ # /;' fb.hg38.chainGCF_019923935.1Link.txt + # 1441231401 bases of 3299210039 (43.684%) in intersection + sed -e 's/^/ # /;' fb.hg38.chainSynGCF_019923935.1Link.txt + # 1373195820 bases of 3299210039 (41.622%) in intersection + + time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -query2Bit="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.2bit" \ +-querySizes="/hive/data/genomes/asmHubs/GCF/019/923/935/GCF_019923935.1/GCF_019923935.1.chrom.sizes.txt" \ + hg38 GCF_019923935.1) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 329m20.127s + + sed -e 's/^/ # /;' fb.hg38.chainRBest.GCF_019923935.1.txt + # 1288371538 bases of 3299210039 (39.051%) in intersection + + ### and for the swap + + cd /hive/data/genomes/asmHubs/allBuild/GCF/019/923/935/GCF_019923935.1_NDDB_SH_1/trackData/blastz.hg38.swap + + time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl -trackHub -noDbNameCheck -swap -verbose=2 \ + -qAsmId GCF_019923935.1_NDDB_SH_1 /hive/data/genomes/hg38/bed/lastzGCF_019923935.1.2023-12-30/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 205m7.620s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainHg38Link.txt + # 1334547184 bases of 2622460639 (50.889%) in intersection + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainSynHg38Link.txt + # 1298033146 bases of 2622460639 (49.497%) in intersection +\ time (~/kent/src/hg/utils/automation/doRecipBest.pl -trackHub -load -workhorse=hgwdev -buildDir=`pwd` \ + \ + -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 hg38) > rbest.log 2>&1 + + grep -w real rbest.log | sed -e 's/^/ # /;' + # real 316m37.285s + + sed -e 's/^/ # /;' fb.GCF_019923935.1.chainRBest.Hg38.txt + # 1289247133 bases of 2622460639 (49.162%) in intersection + +real 1782m42.747s +user 0m2.954s +sys 0m2.951s + +##############################################################################