032903d6adc6d0c49cbedf17c51f4319052cb8ef hiram Thu Apr 16 12:43:59 2026 -0700 improved variable naming fixup problems process in work refs #31811 diff --git src/hg/utils/automation/kegAlignLastz.sh src/hg/utils/automation/kegAlignLastz.sh index 41e88cf8206..2553faabe46 100755 --- src/hg/utils/automation/kegAlignLastz.sh +++ src/hg/utils/automation/kegAlignLastz.sh @@ -1,794 +1,794 @@ #!/bin/bash set -beEu -o pipefail export userName="`whoami`" export bigHub="hgwdev" export workHorse="hgwdev" export smallClusterHub="hgwdev" export fileServer="hgwdev" if [ $# != 4 ]; then printf "ERROR: arg count: %d != 4\n" "$#" 1>&2 printf "usage: kegAlignLastz.sh Where target/query is either a UCSC db name, or is an assembly hub identifier, e.g.: GCA_002844635.1_USMARCv1.0.1 And [tq]Clade is one of: primate|mammal|other Will create directory to work in, for example if, UCSC db: /hive/data/target/bed/lastzQuery.yyyy-mm-dd/ Or, in the assembly hub build directory: /hive/data/genomes/asmHubs/allBuild/GCA/002/844/635/GCA_002844635.1_USMARCv1.0/trackData/lastzQuery.yyyy-mm-dd Will set up a DEF file there, and a run.sh script to run all steps and output makeDoc text to document what happened. AND MORE, it will run the swap operation into the corresponding blastz.target.swap directory in the query genome work space. Email will be sent to: '$userName' upon completion. e.g.: kegAlignLastz.sh rn7 papAnu4 mammal primate\n" 1>&2 exit 255 fi -# asmId - if assembly hub, determine GCx_012345678.9 name +# accId - if assembly hub, determine GCx_012345678.9 name # if not, return the asmName (== UCSC database name) -function asmId() { +function accId() { export asmName=$1 export id="${asmName}" case $asmName in GC[AF]_*) id=`echo $asmName | cut -d'_' -f1-2` ;; *) ;; esac printf "%s" "${id}" } # gcPath - if assembly hub, determine GCx/012/345/678 path # if not return empty string "" (== UCSC database name) function gcPath() { export asmName=$1 export GCxPath="" case $asmName in GC[AF]_*) gcX=`echo $asmName | cut -c1-3` d0=`echo $asmName | cut -c5-7` d1=`echo $asmName | cut -c8-10` d2=`echo $asmName | cut -c11-13` GCxPath="${gcX}/${d0}/${d1}/${d2}" ;; *) ;; esac printf "%s" "${GCxPath}" } # asmSize - determine size of genome function asmSize() { export asmName=$1 export sizes="/hive/data/genomes/${asmName}/chrom.sizes" case $asmName in GC[AF]_*) gcxPath=$(gcPath $asmName) - id=$(asmId $asmName) + id=$(accId $asmName) size=`awk '{sum+=$2}END{print sum}' /hive/data/genomes/asmHubs/${gcxPath}/${id}/${id}.chrom.sizes.txt` ;; *) size=`awk '{sum+=$2}END{print sum}' ${sizes}` ;; esac printf "%s" "${size}" } # seqCount - determine the sequence count in given genome target function seqCount() { export asmName=$1 export sizes="/hive/data/genomes/${asmName}/chrom.sizes" case $asmName in GC[AF]_*) gcxPath=$(gcPath $asmName) - id=$(asmId $asmName) + id=$(accId $asmName) count=`wc -l /hive/data/genomes/asmHubs/${gcxPath}/${id}/${id}.chrom.sizes.txt | cut -d' ' -f1` ;; *) count=`wc -l ${sizes} | cut -d' ' -f1` ;; esac printf "%s" "${count}" } function orgName() { export asmName=$1 case $asmName in GC[AF]_*) gcxPath=$(gcPath $asmName) asmDir="/hive/data/outside/ncbi/genomes/${gcxPath}/${asmName}" asmRpt="${asmDir}/${asmName}_assembly_report.txt" oName=`egrep -m 1 -i "^# organism name:" ${asmRpt} | tr -d '\r' | sed -e 's/.*(//; s/).*//'` ;; *) oName=`hgsql -N -e "select organism from dbDb where name=\"${asmName}\";" hgcentraltest` ;; esac printf "%s" "${oName}" } function faGzUrl() { export asmName=$1 case $asmName in GC[AF]_*) gcxPath=$(gcPath $asmName) - id=$(asmId $asmName) + id=$(accId $asmName) printf "https://hgdownload.soe.ucsc.edu/hubs/%s/%s/%s.fa.gz" "${gcxPath}" "${id}" "${id}" ;; *) printf "https://hgdownload.soe.ucsc.edu/goldenPath/%s/bigZips/%s.fa.gz" "${asmName}" "${asmName}" ;; esac } function orgDate() { export asmName=$1 case $asmName in GC[AF]_*) gcxPath=$(gcPath $asmName) asmDir="/hive/data/outside/ncbi/genomes/${gcxPath}/${asmName}" asmRpt="${asmDir}/${asmName}_assembly_report.txt" oDate=`egrep -m 1 -i "^#[[:space:]]*Date:" ${asmRpt} | tr -d '\r' | sed -e 's/.*ate: \+//;'` ;; *) oDate="" ;; esac printf "%s" "${oDate}" } # check if this database is actually a database browser or a promoted # hub. It could have a MySQL database, but it won't have a chromInfo function promotedHub() { export db=$1 } ############################################################################## ############################################################################## ### start seconds export startT=`date "+%s"` export target="$1" export query="$2" export tClade="$3" export qClade="$4" export tGcPath=$(gcPath $target) export qGcPath=$(gcPath $query) -export tAsmId=$(asmId $target) -export qAsmId=$(asmId $query) +export tAccId=$(accId $target) +export qAccId=$(accId $query) printf "# tq: '${target}' '${query}' '${tClade}' '${qClade}'\n" 1>&2 printf "# tq gcPath: '${tGcPath}' '${qGcPath}'\n" 1>&2 -printf "# tq asmId: '${tAsmId}' '${qAsmId}'\n" 1>&2 +printf "# tq accId: '${tAccId}' '${qAccId}'\n" 1>&2 # upper case first character -export Target="${tAsmId^}" -export Query="${qAsmId^}" +export Target="${tAccId^}" +export Query="${qAccId^}" export DS=`date "+%F"` # assume UCSC db build export buildDir="/hive/data/genomes/${target}/bed/lastz${Query}.${DS}" export targetExists="/hive/data/genomes/${target}/bed" -export symLink="/hive/data/genomes/${target}/bed/lastz.${qAsmId}" -export swapDir="/hive/data/genomes/${query}/bed/blastz.${tAsmId}.swap" +export symLink="/hive/data/genomes/${target}/bed/lastz.${qAccId}" +export swapDir="/hive/data/genomes/${query}/bed/blastz.${tAccId}.swap" export queryExists="/hive/data/genomes/${query}/bed" -export swapLink="/hive/data/genomes/${query}/bed/lastz.${tAsmId}" +export swapLink="/hive/data/genomes/${query}/bed/lastz.${tAccId}" export targetSizes="/hive/data/genomes/${target}/chrom.sizes" export querySizes="/hive/data/genomes/${query}/chrom.sizes" export target2bit="/hive/data/genomes/${target}/${target}.2bit" export query2bit="/hive/data/genomes/${query}/${query}.2bit" export trackHub="" export rBestTrackHub="" export tRbestArgs="" export qRbestArgs="" export tSwapRbestArgs="" export qSwapRbestArgs="" export tFullName="" export qFullName="" export tTdb="xxx" export qTdb="xxx" # override those specifications if assembly hub case $target in GC[AF]_*) trackHub="-trackHub -noDbNameCheck" tFullName="-tAsmId $target" rBestTrackHub="-trackHub" buildDir="/hive/data/genomes/asmHubs/allBuild/${tGcPath}/${target}/trackData/lastz${Query}.${DS}" - symLink="/hive/data/genomes/asmHubs/allBuild/${tGcPath}/${target}/trackData/lastz.${qAsmId}" + symLink="/hive/data/genomes/asmHubs/allBuild/${tGcPath}/${target}/trackData/lastz.${qAccId}" targetExists="/hive/data/genomes/asmHubs/allBuild/${tGcPath}/${target}/trackData" - targetSizes="/hive/data/genomes/asmHubs/${tGcPath}/${tAsmId}/${tAsmId}.chrom.sizes.txt" - target2bit="/hive/data/genomes/asmHubs/${tGcPath}/${tAsmId}/${tAsmId}.2bit" + targetSizes="/hive/data/genomes/asmHubs/${tGcPath}/${tAccId}/${tAccId}.chrom.sizes.txt" + target2bit="/hive/data/genomes/asmHubs/${tGcPath}/${tAccId}/${tAccId}.2bit" tTdb="/hive/data/genomes/asmHubs/allBuild/${tGcPath}/${target}/doTrackDb.bash" tRbestArgs="-target2Bit=\"${target2bit}\" \\ -targetSizes=\"${targetSizes}\"" tSwapRbestArgs="-query2bit=\"${target2bit}\" \\ -querySizes=\"${targetSizes}\"" ;; esac case $query in GC[AF]_*) trackHub="-trackHub -noDbNameCheck" qFullName="-qAsmId $query" rBestTrackHub="-trackHub" - swapDir="/hive/data/genomes/asmHubs/allBuild/${qGcPath}/${query}/trackData/blastz.${tAsmId}.swap" - swapLink="/hive/data/genomes/asmHubs/allBuild/${qGcPath}/${query}/trackData/lastz.${tAsmId}" + swapDir="/hive/data/genomes/asmHubs/allBuild/${qGcPath}/${query}/trackData/blastz.${tAccId}.swap" + swapLink="/hive/data/genomes/asmHubs/allBuild/${qGcPath}/${query}/trackData/lastz.${tAccId}" queryExists="/hive/data/genomes/asmHubs/allBuild/${qGcPath}/${query}/trackData" - querySizes="/hive/data/genomes/asmHubs/${qGcPath}/${qAsmId}/${qAsmId}.chrom.sizes.txt" - query2bit="/hive/data/genomes/asmHubs/${qGcPath}/${qAsmId}/${qAsmId}.2bit" + querySizes="/hive/data/genomes/asmHubs/${qGcPath}/${qAccId}/${qAccId}.chrom.sizes.txt" + query2bit="/hive/data/genomes/asmHubs/${qGcPath}/${qAccId}/${qAccId}.2bit" qTdb="/hive/data/genomes/asmHubs/allBuild/${qGcPath}/${query}/doTrackDb.bash" qRbestArgs="-query2Bit=\"${query2bit}\" \\ -querySizes=\"${querySizes}\"" qSwapRbestArgs="-target2bit=\"${query2bit}\" \\ -targetSizes=\"${querySizes}\"" ;; esac if [ ! -d "${targetExists}" ]; then printf "ERROR: can not find ${targetExists}\n" 1>&2 exit 255 fi if [ ! -d "${queryExists}" ]; then printf "ERROR: can not find ${queryExists}\n" 1>&2 exit 255 fi if [ ! -s "${target2bit}" ]; then printf "ERROR: can not find ${target2bit}\n" 1>&2 exit 255 fi if [ ! -s "${query2bit}" ]; then printf "ERROR: can not find ${query2bit}\n" 1>&2 exit 255 fi if [ ! -s "${targetSizes}" ]; then printf "ERROR: can not find ${targetSizes}\n" 1>&2 exit 255 fi if [ ! -s "${querySizes}" ]; then printf "ERROR: can not find ${querySizes}\n" 1>&2 exit 255 fi export doneCount=0 export primaryDone=0 export swapDone=0 if [ -L "${symLink}" ]; then printf "# ${query} -> ${target} already done\n" 1>&2 doneCount=`echo $doneCount | awk '{printf "%d", $1+1}'` primaryDone=1 else printf "# primaryDone $primaryDone no symLink: $symLink\n" 1>&2 fi if [ -L "${swapLink}" ]; then printf "# swap ${query} -> ${target} already done\n" 1>&2 doneCount=`echo $doneCount | awk '{printf "%d", $1+1}'` swapDone=1 fi export working=`ls -d ${targetExists}/lastz${Query}.* 2> /dev/null | wc -l` if [ "${working}" -gt 0 ]; then if [ "${primaryDone}" -eq 0 ]; then printf "# in progress, ${query} -> ${target}:\n" 1>&2 printf "# " 1>&2 ls -ogd ${targetExists}/lastz${Query}.* 1>&2 fi buildDir=`ls -d ${targetExists}/lastz${Query}.* | tail -1` printf "# continuing: %s\n" "${buildDir}" 1>&2 fi export primaryPartsDone=`ls $buildDir/fb.* 2> /dev/null | wc -l` if [ "$primaryPartsDone" -gt 0 ]; then primaryDone="$primaryPartsDone" printf "# primaryPartsDone $primaryPartsDone primaryDone $primaryDone\n" 1>&2 fi if [ -d "${swapDir}" ]; then printf "# swap in progress ${query} -> ${target}\n" 1>&2 printf "# " 1>&2 ls -ogd "${swapDir}" 1>&2 if [ "${doneCount}" -ne 2 ]; then printf "# doneCount $doneCount -ne 2 exit 0 since swap in progress\n" 1>&2 exit 0 fi fi if [ "${doneCount}" -eq 2 ]; then printf "# all done\n" 1>&2 fi export tOrgName="$(orgName $target)" export qOrgName="$(orgName $query)" export tOrgDate="$(orgDate $target)" export qOrgDate="$(orgDate $query)" export tAsmSize="$(asmSize $target)" export qAsmSize="$(asmSize $query)" export tSequenceCount="$(seqCount $target)" export qSequenceCount="$(seqCount $query)" export tFaGzUrl="$(faGzUrl $target)" export qFaGzUrl="$(faGzUrl $query)" printf "# working: %s\n" "${buildDir}" 1>&2 printf "# target: $target - $tOrgName - $tOrgDate - $tClade - $tSequenceCount sequences\n" 1>&2 printf "# query: $query - $qOrgName - $qOrgDate - $qClade - $qSequenceCount sequences\n" 1>&2 LC_NUMERIC=en_US printf "# sizes: target: %'d - query: %'d\n" "${tAsmSize}" "${qAsmSize}" 1>&2 export seq1Limit="40" if [ "${tSequenceCount}" -gt 50000 ]; then seq1Limit="100" fi export seq2Limit="100" if [ "${qSequenceCount}" -gt 50000 ]; then seq2Limit="500" fi export minScore="3000" export linearGap="medium" case $tClade in "primate") case $qClade in "primate") minScore="5000" ;; "mammal") ;; "other") minScore="5000" linearGap="loose" ;; esac ;; "mammal") case $qClade in "primate") ;; "mammal") ;; "other") minScore="5000" linearGap="loose" ;; esac ;; "other") minScore="5000" linearGap="loose" esac if [ "$tClade" == "primate" -a "$qClade" == "primate" ]; then -export yamlString="# ${target}.${query}.yaml +export yamlString="# ${tAccId}.${qAccId}.yaml TARGET_Sequence: class: File path: ${tFaGzUrl} QUERY_Sequence: class: File path: ${qFaGzUrl} # axtChain options axtChainMinScore: ${minScore} linear_gap_options.linear_gap: ${linearGap} # lastz options xdropX: 910 ydropY: 15000 stepZ: 1 noTransitionT: false strand_selectorB: both seeding_options.seed_selector: 12of19 hspthreshK: 4500 gappedthreshL: 4500 innerH: 2000 " export defString="# ${qOrgName} ${Query} vs. ${tOrgName} ${Target} BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz BLASTZ_T=2 BLASTZ_O=600 BLASTZ_E=150 BLASTZ_M=254 BLASTZ_K=4500 BLASTZ_Y=15000 BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q # A C G T # A 90 -330 -236 -356 # C -330 100 -318 -236 # G -236 -318 100 -330 # T -356 -236 -330 90 # TARGET: ${tOrgName} ${tOrgDate} ${target} SEQ1_DIR=${target2bit} SEQ1_LEN=${targetSizes} SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=${seq1Limit} # QUERY: ${qOrgName} ${qOrgDate} ${query} SEQ2_DIR=${query2bit} SEQ2_LEN=${querySizes} SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=${seq2Limit} BASE=${buildDir} TMPDIR=/dev/shm " else export yamlString="# ${target}.${query}.yaml TARGET_Sequence: class: File path: ${tFaGzUrl} QUERY_Sequence: class: File path: ${qFaGzUrl} # axtChain options axtChainMinScore: ${minScore} linear_gap_options.linear_gap: ${linearGap} # lastz options xdropX: 910 ydropY: 9400 stepZ: 1 noTransitionT: true strand_selectorB: both seeding_options.seed_selector: 12of19 hspthreshK: 3000 gappedthreshL: 3000 innerH: 2000 " export defString="# ${qOrgName} ${Query} vs. ${tOrgName} ${Target} BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz # TARGET: ${tOrgName} ${tOrgDate} ${target} SEQ1_DIR=${target2bit} SEQ1_LEN=${targetSizes} SEQ1_CHUNK=20000000 SEQ1_LAP=10000 SEQ1_LIMIT=${seq1Limit} # QUERY: ${qOrgName} ${qOrgDate} ${query} SEQ2_DIR=${query2bit} SEQ2_LEN=${querySizes} SEQ2_CHUNK=20000000 SEQ2_LAP=0 SEQ2_LIMIT=${seq2Limit} BASE=${buildDir} TMPDIR=/dev/shm " fi ### skip primary alignment if it is already done ### primaryDone == 0 means NOT done yet if [ $primaryDone -eq 0 ]; then mkdir "${buildDir}" ### setup the DEF file printf "%s" "${defString}" > ${buildDir}/DEF ### and the yaml file -printf "%s" "${yamlString}" > ${buildDir}/${tAsmId}.${qAsmId}.yaml +printf "%s" "${yamlString}" > ${buildDir}/${tAccId}.${qAccId}.yaml ### setup the buildDir/run.sh script printf "#!/bin/bash set -beEu -o pipefail export buildDir=\"${buildDir}\" export swapDir=\"${swapDir}\" export PM=\"/hive/users/hiram/galaxy/venv3.12/bin/planemo\" -export targetDb=\"${tAsmId}\" -export queryDb=\"${qAsmId}\" +export targetDb=\"${tAccId}\" +export queryDb=\"${qAccId}\" export QueryDb=\"${Query}\" cd \${buildDir} mkdir -p log -export DS=\`date \"+\%%F_\%%T_\%%s\"\` +export DS=\`date \"+%%F_%%T_%%s\"\` export logDir=\"\${buildDir}/log\" export logFile=\"\${logDir}/\${DS}.log\" time (\${PM} run \\ - \"~/kent/src/hg/utils/automation/kegAlign.json.gz\" \\ + ~/kent/src/hg/utils/automation/kegAlign.json.ga \\ \"\${targetDb}.\${queryDb}.yaml\" --profile vgp \\ --history_name \"\${targetDb}.\${queryDb}.kegAlign\" \\ --test_output_json \"\${logDir}/runOutput.\${DS}.json\") >> \"\${logFile}\" 2>&1 export invocationId=\`jq '.tests[0].data.invocation_details.details.invocation_id' \"\${logDir}/runOutput.\${DS}.json\" | tr -d '\"'\` printf \"invocation ID: %%s\\n\" \"\${invocationId}\" 1>&2 mkdir -p result/\${DS} \${PM} invocation_download \"\${invocationId}\" --profile vgp \\ --output_directory result/\${DS} ### install allChain into buildDir/axtChain/ mkdir -p \${buildDir}/axtChain export allChainFile=\`ls result/\${DS}/allChain__*.chain\` gzip -c \"\${allChainFile}\" > \${buildDir}/axtChain/\${targetDb}.\${queryDb}.all.chain.gz ### convert target allChain to bigBed and measure featureBits cd \${buildDir}/axtChain export tSizes=\"${targetSizes}\" export allChain=\"\${targetDb}.\${queryDb}.all.chain.gz\" hgLoadChain -test -noBin -tIndex \${targetDb} allChain \"\${allChain}\" sed 's/.000000//' chain.tab | awk 'BEGIN {OFS=\"\\t\"} {print \\\$2, \\\$4, \\\$5, \\\$11, 1000, \\\$8, \\\$3, \\\$6, \\\$7, \\\$9, \\\$10, \\\$1}' > allChain.tab awk 'BEGIN {OFS=\"\\t\"} {print \\\$1, \\\$2, \\\$3, \\\$5, \\\$4}' link.tab | sort -k1,1 -k2,2n > allChainLink.tab bedToBigBed -type=bed6+6 -as=~/kent/src/hg/lib/bigChain.as -tab allChain.tab \${tSizes} allChain.bb bedToBigBed -type=bed4+1 -as=~/kent/src/hg/lib/bigLink.as -tab allChainLink.tab \${tSizes} allChainLink.bb rm -f allChain.tab allChainLink.tab chain.tab link.tab export totalBases=\`ave -col=2 \${tSizes} | grep \"^total\" | awk '{printf \"%d\", \\\$2}'\` export basesCovered=\`bigBedInfo allChainLink.bb | grep \"basesCovered\" | cut -d' ' -f2 | tr -d ','\` export percentCovered=\`echo \${basesCovered} \${totalBases} | awk '{printf \"%.3f\", 100.0*\\\$1/\\\$2}'\` printf \"%d bases of %d (%s%%%%) in intersection\\n\" \"\${basesCovered}\" \"\${totalBases}\" \"\${percentCovered}\" > \${buildDir}/fb.\${targetDb}.chain\${QueryDb}Link.txt cat \${buildDir}/fb.\${targetDb}.chain\${QueryDb}Link.txt ### install netChainSubset (over.chain) for target cd \${buildDir} export overChainFile=\`ls result/\${DS}/'netChainSubset on dataset 7 and 21__'*.chain\` gzip -c \"\${overChainFile}\" > \${buildDir}/axtChain/\${targetDb}.\${queryDb}.over.chain.gz ### convert target over.chain to bigBed and measure featureBits cd \${buildDir}/axtChain export overChain=\"\${targetDb}.\${queryDb}.over.chain.gz\" hgLoadChain -test -noBin -tIndex \${targetDb} overChain \"\${overChain}\" sed 's/.000000//' chain.tab | awk 'BEGIN {OFS=\"\\t\"} {print \\\$2, \\\$4, \\\$5, \\\$11, 1000, \\\$8, \\\$3, \\\$6, \\\$7, \\\$9, \\\$10, \\\$1}' > overChain.tab awk 'BEGIN {OFS=\"\\t\"} {print \\\$1, \\\$2, \\\$3, \\\$5, \\\$4}' link.tab | sort -k1,1 -k2,2n > overChainLink.tab bedToBigBed -type=bed6+6 -as=~/kent/src/hg/lib/bigChain.as -tab overChain.tab \${tSizes} overChain.bb bedToBigBed -type=bed4+1 -as=~/kent/src/hg/lib/bigLink.as -tab overChainLink.tab \${tSizes} overChainLink.bb rm -f overChain.tab overChainLink.tab chain.tab link.tab export totalBases=\`ave -col=2 \${tSizes} | grep \"^total\" | awk '{printf \"%d\", \\\$2}'\` export basesCovered=\`bigBedInfo overChainLink.bb | grep \"basesCovered\" | cut -d' ' -f2 | tr -d ','\` export percentCovered=\`echo \${basesCovered} \${totalBases} | awk '{printf \"%.3f\", 100.0*\\\$1/\\\$2}'\` printf \"%d bases of %d (%s%%%%) in intersection\\n\" \"\${basesCovered}\" \"\${totalBases}\" \"\${percentCovered}\" > \${buildDir}/fb.\${targetDb}.chainSyn\${QueryDb}Link.txt cat \${buildDir}/fb.\${targetDb}.chainSyn\${QueryDb}Link.txt ### install allChainSwap into swapDir/axtChain/ mkdir -p \${swapDir}/axtChain cd \${buildDir} export allChainSwapFile=\`ls result/\${DS}/allChainSwap__*.chain\` gzip -c \"\${allChainSwapFile}\" > \${swapDir}/axtChain/\${queryDb}.\${targetDb}.all.chain.gz ### convert swap allChain to bigBed and measure featureBits cd \${swapDir}/axtChain export qSizes=\"${querySizes}\" export allChain=\"\${queryDb}.\${targetDb}.all.chain.gz\" hgLoadChain -test -noBin -tIndex \${queryDb} allChain \"\${allChain}\" sed 's/.000000//' chain.tab | awk 'BEGIN {OFS=\"\\t\"} {print \\\$2, \\\$4, \\\$5, \\\$11, 1000, \\\$8, \\\$3, \\\$6, \\\$7, \\\$9, \\\$10, \\\$1}' > allChain.tab awk 'BEGIN {OFS=\"\\t\"} {print \\\$1, \\\$2, \\\$3, \\\$5, \\\$4}' link.tab | sort -k1,1 -k2,2n > allChainLink.tab bedToBigBed -type=bed6+6 -as=~/kent/src/hg/lib/bigChain.as -tab allChain.tab \${qSizes} allChain.bb bedToBigBed -type=bed4+1 -as=~/kent/src/hg/lib/bigLink.as -tab allChainLink.tab \${qSizes} allChainLink.bb rm -f allChain.tab allChainLink.tab chain.tab link.tab export totalBases=\`ave -col=2 \${qSizes} | grep \"^total\" | awk '{printf \"%d\", \\\$2}'\` export basesCovered=\`bigBedInfo allChainLink.bb | grep \"basesCovered\" | cut -d' ' -f2 | tr -d ','\` export percentCovered=\`echo \${basesCovered} \${totalBases} | awk '{printf \"%.3f\", 100.0*\\\$1/\\\$2}'\` export Target=\"${Target}\" printf \"%d bases of %d (%s%%%%) in intersection\\n\" \"\${basesCovered}\" \"\${totalBases}\" \"\${percentCovered}\" > \${swapDir}/fb.\${queryDb}.chain\${Target}Link.txt cat \${swapDir}/fb.\${queryDb}.chain\${Target}Link.txt ### install netChainSubset (over.chain) for swap cd \${buildDir} export overChainSwapFile=\`ls result/\${DS}/'netChainSubset on dataset 8 and 35__'*.chain\` gzip -c \"\${overChainSwapFile}\" > \${swapDir}/axtChain/\${queryDb}.\${targetDb}.over.chain.gz ### convert swap over.chain to bigBed and measure featureBits cd \${swapDir}/axtChain export overChain=\"\${queryDb}.\${targetDb}.over.chain.gz\" hgLoadChain -test -noBin -tIndex \${queryDb} overChain \"\${overChain}\" sed 's/.000000//' chain.tab | awk 'BEGIN {OFS=\"\\t\"} {print \\\$2, \\\$4, \\\$5, \\\$11, 1000, \\\$8, \\\$3, \\\$6, \\\$7, \\\$9, \\\$10, \\\$1}' > overChain.tab awk 'BEGIN {OFS=\"\\t\"} {print \\\$1, \\\$2, \\\$3, \\\$5, \\\$4}' link.tab | sort -k1,1 -k2,2n > overChainLink.tab bedToBigBed -type=bed6+6 -as=~/kent/src/hg/lib/bigChain.as -tab overChain.tab \${qSizes} overChain.bb bedToBigBed -type=bed4+1 -as=~/kent/src/hg/lib/bigLink.as -tab overChainLink.tab \${qSizes} overChainLink.bb rm -f overChain.tab overChainLink.tab chain.tab link.tab export totalBases=\`ave -col=2 \${qSizes} | grep \"^total\" | awk '{printf \"%d\", \\\$2}'\` export basesCovered=\`bigBedInfo overChainLink.bb | grep \"basesCovered\" | cut -d' ' -f2 | tr -d ','\` export percentCovered=\`echo \${basesCovered} \${totalBases} | awk '{printf \"%.3f\", 100.0*\\\$1/\\\$2}'\` printf \"%d bases of %d (%s%%%%) in intersection\\n\" \"\${basesCovered}\" \"\${totalBases}\" \"\${percentCovered}\" > \${swapDir}/fb.\${queryDb}.chainSyn\${Target}Link.txt cat \${swapDir}/fb.\${queryDb}.chainSyn\${Target}Link.txt " > ${buildDir}/run.sh chmod +x ${buildDir}/run.sh ### run the primary alignment printf "running: time (${buildDir}/run.sh) >> ${buildDir}/do.log 2>&1\n" 1>&2 # time (${buildDir}/run.sh) >> ${buildDir}/do.log 2>&1 exit $? ### typical contents of the invocation_download: ### ls result/2026-04-02_16:00:02_1775170802 ### 'Batched LASTZ on dataset 5__70a08f89-a77d-4333-b425-b13959e40d1b.axt' ### 'KegAlign on dataset 3 and 4__a32df3e9-13d0-4c5e-b765-df69c657ae89.tgz' ### allChainSwap__5e11f323-58fc-43f9-afbd-6cff21f0e7af.chain ### allChain__74038a6d-d735-4784-8b17-31a25ddbb036.chain ###'netChainSubset on dataset 7 and 21__72cbd3a9-4136-4e72-86c9-9da0c230c5d0.chain' ###'netChainSubset on dataset 8 and 35__9acc344f-19da-4ef9-a578-7282940badc0.chain' # rebuild trackDb if possible here if [ -x "${tTdb}" ]; then ${tTdb} else printf "# do not find tTdb '%s'\n" "${tTdb}" 1>&2 fi fi ### if [ $primaryDone -eq 0 ]; then exit $? #### print out the makeDoc.txt to this point into buildDir/makeDoc.txt printf "############################################################################## # kegAlign LASTZ ${tOrgName} ${Target} vs. $qOrgName ${Query} # (DONE - $DS - $userName) mkdir $buildDir cd $buildDir printf '${yamlString} ' > DEF time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl ${trackHub} -verbose=2 \`pwd\`/DEF -syntenicNet \\ ${tFullName} ${qFullName} -workhorse=${workHorse} -smallClusterHub=${smallClusterHub} -fileServer=${fileServer} -bigClusterHub=${bigHub} \\ -chainMinScore=${minScore} -chainLinearGap=${linearGap}) > do.log 2>&1 grep -w real do.log | sed -e 's/^/ # /;' " > ${buildDir}/makeDoc.txt (grep -w real $buildDir/do.log || true) | sed -e 's/^/ # /;' | head -1 >> ${buildDir}/makeDoc.txt -printf "\n sed -e 's/^/ # /;' fb.${tAsmId}.chain${Query}Link.txt\n" >> ${buildDir}/makeDoc.txt -sed -e 's/^/ # /;' $buildDir/fb.${tAsmId}.chain${Query}Link.txt >> ${buildDir}/makeDoc.txt +printf "\n sed -e 's/^/ # /;' fb.${tAccId}.chain${Query}Link.txt\n" >> ${buildDir}/makeDoc.txt +sed -e 's/^/ # /;' $buildDir/fb.${tAccId}.chain${Query}Link.txt >> ${buildDir}/makeDoc.txt -printf " sed -e 's/^/ # /;' fb.${tAsmId}.chainSyn${Query}Link.txt\n" >> ${buildDir}/makeDoc.txt -sed -e 's/^/ # /;' $buildDir/fb.${tAsmId}.chainSyn${Query}Link.txt >> ${buildDir}/makeDoc.txt +printf " sed -e 's/^/ # /;' fb.${tAccId}.chainSyn${Query}Link.txt\n" >> ${buildDir}/makeDoc.txt +sed -e 's/^/ # /;' $buildDir/fb.${tAccId}.chainSyn${Query}Link.txt >> ${buildDir}/makeDoc.txt printf "\n time (~/kent/src/hg/utils/automation/doRecipBest.pl ${rBestTrackHub} -load -workhorse=${workHorse} -buildDir=\`pwd\` \\ ${tRbestArgs} \\ ${qRbestArgs} \\ - ${tAsmId} ${qAsmId}) > rbest.log 2>&1 + ${tAccId} ${qAccId}) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;'\n" >> ${buildDir}/makeDoc.txt (grep -w real $buildDir/rbest.log || true) | sed -e 's/^/ # /;' >> ${buildDir}/makeDoc.txt -printf "\n sed -e 's/^/ # /;' fb.${tAsmId}.chainRBest.${Query}.txt\n" >> ${buildDir}/makeDoc.txt -(sed -e 's/^/ # /;' ${buildDir}/fb.${tAsmId}.chainRBest.${Query}.txt || true) >> ${buildDir}/makeDoc.txt +printf "\n sed -e 's/^/ # /;' fb.${tAccId}.chainRBest.${Query}.txt\n" >> ${buildDir}/makeDoc.txt +(sed -e 's/^/ # /;' ${buildDir}/fb.${tAccId}.chainRBest.${Query}.txt || true) >> ${buildDir}/makeDoc.txt printf "\n ### and for the swap\n" >> ${buildDir}/makeDoc.txt cat ${buildDir}/makeDoc.txt printf "# swap into: ${swapDir}\n" 1>&2 if [ "$swapDone" -eq 0 ]; then mkdir ${swapDir} ln -s ${buildDir}/DEF ${swapDir}/DEF printf "#!/bin/bash set -beEu -o pipefail cd $swapDir -export targetDb=\"${tAsmId}\" +export targetDb=\"${tAccId}\" export Target=\"${Target}\" -export queryDb=\"${qAsmId}\" +export queryDb=\"${qAccId}\" time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl ${trackHub} -swap -verbose=2 \\ ${tFullName} ${qFullName} ${buildDir}/DEF -swapDir=\`pwd\` \\ -syntenicNet -workhorse=${workHorse} -smallClusterHub=${smallClusterHub} -fileServer=${fileServer} -bigClusterHub=${bigHub} \\ -chainMinScore=${minScore} -chainLinearGap=${linearGap}) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' sed -e 's/^/ # /;' fb.\${queryDb}.chain\${Target}Link.txt sed -e 's/^/ # /;' fb.\${queryDb}.chainSyn\${Target}Link.txt time (~/kent/src/hg/utils/automation/doRecipBest.pl ${rBestTrackHub} -load -workhorse=${workHorse} -buildDir=\`pwd\` \\ ${tSwapRbestArgs} \\ ${qSwapRbestArgs} \\ \${queryDb} \${targetDb}) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;' sed -e 's/^/ # /;' fb.\${queryDb}.chainRBest.\${Target}.txt " > ${swapDir}/runSwap.sh chmod +x ${swapDir}/runSwap.sh printf "# running ${swapDir}/runSwap.sh\n" 1>&2 time (${swapDir}/runSwap.sh) >> ${swapDir}/doSwap.log 2>&1 # rebuild trackDb if possible here if [ -x "${qTdb}" ]; then ${qTdb} else printf "# do not find qTdb '%s'\n" "${qTdb}" 1>&2 fi fi ### if [ "$swapDone" -eq 0 ]; then ### continue the make doc printf "\n cd ${swapDir}\n" >> ${buildDir}/makeDoc.txt printf "\n time (~/kent/src/hg/utils/automation/doBlastzChainNet.pl ${trackHub} -swap -verbose=2 \\ ${tFullName} ${qFullName} ${buildDir}/DEF -swapDir=\`pwd\` \\ -syntenicNet -workhorse=${workHorse} -smallClusterHub=${smallClusterHub} -fileServer=${fileServer} -bigClusterHub=${bigHub} \\ -chainMinScore=${minScore} -chainLinearGap=${linearGap}) > swap.log 2>&1 grep -w real swap.log | sed -e 's/^/ # /;' " >> ${buildDir}/makeDoc.txt (grep -w real ${swapDir}/swap.log || true) | sed -e 's/^/ # /;' >> ${buildDir}/makeDoc.txt -printf "\n sed -e 's/^/ # /;' fb.${qAsmId}.chain${Target}Link.txt\n" >> ${buildDir}/makeDoc.txt -sed -e 's/^/ # /;' ${swapDir}/fb.${qAsmId}.chain${Target}Link.txt >> ${buildDir}/makeDoc.txt +printf "\n sed -e 's/^/ # /;' fb.${qAccId}.chain${Target}Link.txt\n" >> ${buildDir}/makeDoc.txt +sed -e 's/^/ # /;' ${swapDir}/fb.${qAccId}.chain${Target}Link.txt >> ${buildDir}/makeDoc.txt -printf " sed -e 's/^/ # /;' fb.${qAsmId}.chainSyn${Target}Link.txt\n" >> ${buildDir}/makeDoc.txt -sed -e 's/^/ # /;' ${swapDir}/fb.${qAsmId}.chainSyn${Target}Link.txt >> ${buildDir}/makeDoc.txt +printf " sed -e 's/^/ # /;' fb.${qAccId}.chainSyn${Target}Link.txt\n" >> ${buildDir}/makeDoc.txt +sed -e 's/^/ # /;' ${swapDir}/fb.${qAccId}.chainSyn${Target}Link.txt >> ${buildDir}/makeDoc.txt printf "\ time (~/kent/src/hg/utils/automation/doRecipBest.pl ${rBestTrackHub} -load -workhorse=${workHorse} -buildDir=\`pwd\` \\ ${tSwapRbestArgs} \\ ${qSwapRbestArgs} \\ - ${qAsmId} ${tAsmId}) > rbest.log 2>&1 + ${qAccId} ${tAccId}) > rbest.log 2>&1 grep -w real rbest.log | sed -e 's/^/ # /;'\n" >> ${buildDir}/makeDoc.txt (grep -w real ${swapDir}/rbest.log || true) | sed -e 's/^/ # /;' >> ${buildDir}/makeDoc.txt -printf "\n sed -e 's/^/ # /;' fb.${qAsmId}.chainRBest.${Target}.txt\n" >> ${buildDir}/makeDoc.txt -(sed -e 's/^/ # /;' ${swapDir}/fb.${qAsmId}.chainRBest.${Target}.txt || true) >> ${buildDir}/makeDoc.txt +printf "\n sed -e 's/^/ # /;' fb.${qAccId}.chainRBest.${Target}.txt\n" >> ${buildDir}/makeDoc.txt +(sed -e 's/^/ # /;' ${swapDir}/fb.${qAccId}.chainRBest.${Target}.txt || true) >> ${buildDir}/makeDoc.txt printf "\n##############################################################################\n" >> ${buildDir}/makeDoc.txt ### show completed makeDoc.txt #### cat ${buildDir}/makeDoc.txt ### end seconds export endT=`date "+%s"` export toAddress="$userName" export fromAddress="$userName" export subject="kegAlign lastz DONE $target $query" printf "To: $toAddress From: $fromAddress Subject: $subject ################################################################## " > /tmp/send.txt.$$ date >> /tmp/send.txt.$$ printf "##################################################################\n" >> /tmp/send.txt.$$ cat ${buildDir}/makeDoc.txt >> /tmp/send.txt.$$ ### show elapsed time printf "%s\t%s\n" "${endT}" "${startT}" | awk -F$'\t' '{ seconds=$1-$2 hours=int(seconds/3600) minutes=int((seconds-(hours*3600))/60) s=seconds % 60 printf "### elapsed time: %02dh %02dm %02ds\n\n", hours, minutes, s }' >> /tmp/send.txt.$$ date >> /tmp/send.txt.$$ printf "##################################################################\n" >> /tmp/send.txt.$$ cat /tmp/send.txt.$$ | /usr/sbin/sendmail -t -oi rm -f /tmp/send.txt.$$