c078aaab1bcbfbc23b26931b850430af6f352c3f
hiram
  Sun Apr 19 10:41:30 2026 -0700
correctly naming the liftOver and liftOverSwap file outputs refs #31811

diff --git src/hg/utils/automation/kegAlignLastz.sh src/hg/utils/automation/kegAlignLastz.sh
index d99ca5ca12a..30c2c99a0c0 100755
--- src/hg/utils/automation/kegAlignLastz.sh
+++ src/hg/utils/automation/kegAlignLastz.sh
@@ -188,34 +188,34 @@
 
 export target="$1"
 export query="$2"
 export tClade="$3"
 export qClade="$4"
 
 export tGcPath=$(gcPath $target)
 export qGcPath=$(gcPath $query)
 export tAccId=$(accId $target)
 export qAccId=$(accId $query)
 
 # verify GenArk assemblies exist in hgcentraltest.genark unless -force
 if [ "$forceRun" -eq 0 ]; then
   export genarkErrors=0
   case $target in
-    GC[AF]_*) verifyGenark "$tAsmId" "$target" || genarkErrors=$((genarkErrors+1)) ;;
+    GC[AF]_*) verifyGenark "$tAccId" "$target" || genarkErrors=$((genarkErrors+1)) ;;
   esac
   case $query in
-    GC[AF]_*) verifyGenark "$qAsmId" "$query" || genarkErrors=$((genarkErrors+1)) ;;
+    GC[AF]_*) verifyGenark "$qAccId" "$query" || genarkErrors=$((genarkErrors+1)) ;;
   esac
   if [ "$genarkErrors" -gt 0 ]; then
     printf "Use -force to skip this check\n" 1>&2
     exit 255
   fi
 fi
 
 printf "# tq: '${target}' '${query}' '${tClade}' '${qClade}'\n" 1>&2
 printf "# tq gcPath: '${tGcPath}' '${qGcPath}'\n" 1>&2
 printf "# tq accId: '${tAccId}' '${qAccId}'\n" 1>&2
 
 # upper case first character
 export Target="${tAccId^}"
 export Query="${qAccId^}"
 
@@ -636,87 +636,87 @@
              --test_output_json \"\${logDir}/runOutput.\${DS}.json\") >> \"\${logFile}\" 2>&1
 
   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}
   # record the invocation ID and associated log file name
   printf \"%%s\\tinvocation ID: %%s\\t%%s\\n\" \"\${DS}\" \"\${invocationId}\" \"\${logDir}/runOutput.\${DS}.json\" > successInvocationId.txt
 fi
 ### use that runOutput log file to get the history ID for deletion
 
 ### install allChain into buildDir/axtChain/
 mkdir -p \${buildDir}/axtChain
 if [ ! -s \"\${buildDir}/axtChain/\${targetDb}.\${queryDb}.all.chain.gz\" ]; then
-  allChainFile=\`ls result/\${DS}/allChain__*.chain\`
+  allChainFile=\`ls result/\${DS}/allChain__.*.chain\`
   gzip -c \"\${allChainFile}\" > \${buildDir}/axtChain/\${targetDb}.\${queryDb}.all.chain.gz
 fi
 
 ### convert target allChain to bigBed and measure featureBits
 cd \${buildDir}/axtChain
 if [ ! -s \"\${buildDir}/fb.\${targetDb}.chain\${QueryDb}Link.txt\" ]; then
   allChain=\"\${targetDb}.\${queryDb}.all.chain.gz\"
   chainBigBedFb \${targetDb} chain\${QueryDb} \${allChain} \${tSizes} \${buildDir}/fb.\${targetDb}.chain\${QueryDb}Link.txt
 fi
 cat \"\${buildDir}/fb.\${targetDb}.chain\${QueryDb}Link.txt\" 1>&2
 
 ### install netChainSubset (over.chain) for target
 cd \${buildDir}
 if [ ! -s \"\${buildDir}/axtChain/\${targetDb}.\${queryDb}.over.chain.gz\" ]; then
-  overChainFile=\`ls result/\${DS}/'netChainSubset on dataset 8 and 22__'*.chain\`
+  overChainFile=\`ls result/\${DS}/liftOverChain_.*.chain\`
   gzip -c \"\${overChainFile}\" > \${buildDir}/axtChain/\${targetDb}.\${queryDb}.over.chain.gz
 fi
 
 ### convert target over.chain to bigBed and measure featureBits
 cd \${buildDir}/axtChain
-if [ ! -s \"\${buildDir}/fb.\${targetDb}.chain\${QueryDb}Link.txt\" ]; then
+if [ ! -s \"\${buildDir}/fb.\${targetDb}.chainLiftOver\${QueryDb}Link.txt\" ]; then
   overChain=\"\${targetDb}.\${queryDb}.over.chain.gz\"
-  chainBigBedFb \${targetDb} chainLiftOver\${QueryDb} \${overChain} \${tSizes} \${buildDir}/fb.\${targetDb}.chain\${QueryDb}Link.txt
+  chainBigBedFb \${targetDb} chainLiftOver\${QueryDb} \${overChain} \${tSizes} \${buildDir}/fb.\${targetDb}.chainLiftOver\${QueryDb}Link.txt
 fi
-cat \"\${buildDir}/fb.\${targetDb}.chain\${QueryDb}Link.txt\" 1>&2
+cat \"\${buildDir}/fb.\${targetDb}.chainLiftOver\${QueryDb}Link.txt\" 1>&2
 
 ### install allChainSwap into swapDir/axtChain/
 mkdir -p \${swapDir}/axtChain
 cd \${buildDir}
 if [ ! -s \"\${swapDir}/axtChain/\${queryDb}.\${targetDb}.all.chain.gz\" ]; then
-  allChainSwapFile=\`ls result/\${DS}/allChainSwap__*.chain\`
+  allChainSwapFile=\`ls result/\${DS}/allChainSwap_.*.chain\`
   gzip -c \"\${allChainSwapFile}\" > \${swapDir}/axtChain/\${queryDb}.\${targetDb}.all.chain.gz
 fi
 
 ### convert swap allChain to bigBed and measure featureBits
 cd \${swapDir}/axtChain
 if [ ! -s \"\${swapDir}/fb.\${queryDb}.chain\${Target}Link.txt\" ]; then
   allChain=\"\${queryDb}.\${targetDb}.all.chain.gz\"
   chainBigBedFb \${queryDb} chain\${TargetDb} \${allChain} \${qSizes} \${swapDir}/fb.\${queryDb}.chain\${Target}Link.txt
 fi
 cat \"\${swapDir}/fb.\${queryDb}.chain\${Target}Link.txt\" 1>&2
 
 ### install netChainSubset (over.chain) for swap
 cd \${buildDir}
 if [ ! -s \"\${swapDir}/axtChain/\${queryDb}.\${targetDb}.over.chain.gz\" ]; then
-  overChainSwapFile=\`ls result/\${DS}/'netChainSubset on dataset 9 and 36__'*.chain\`
+  overChainSwapFile=\`ls result/\${DS}/swapLiftOverChain_.*.chain\`
   gzip -c \"\${overChainSwapFile}\" > \${swapDir}/axtChain/\${queryDb}.\${targetDb}.over.chain.gz
 fi
 
 ### convert swap over.chain to bigBed and measure featureBits
 cd \${swapDir}/axtChain
-if [ ! -s \"\${swapDir}/fb.\${queryDb}.chain\${Target}Link.txt\" ]; then
+if [ ! -s \"\${swapDir}/fb.\${queryDb}.chainLiftOver\${Target}Link.txt\" ]; then
   overChain=\"\${queryDb}.\${targetDb}.over.chain.gz\"
-  chainBigBedFb \${queryDb} chainLiftOver\${TargetDb} \${overChain} \${qSizes} \${swapDir}/fb.\${queryDb}.chain\${Target}Link.txt
+  chainBigBedFb \${queryDb} chainLiftOver\${TargetDb} \${overChain} \${qSizes} \${swapDir}/fb.\${queryDb}.chainLiftOver\${Target}Link.txt
 fi
-cat \"\${swapDir}/fb.\${queryDb}.chain\${Target}Link.txt\" 1>&2
+cat \"\${swapDir}/fb.\${queryDb}.chainLiftOver\${Target}Link.txt\" 1>&2
 
 " > ${buildDir}/kegAlign.sh
 chmod +x ${buildDir}/kegAlign.sh
 
 ### run the primary alignment, galaxy kegAlign style
 printf "running: time (${buildDir}/kegAlign.sh) >> ${buildDir}/kegAlign.log 2>&1\n" 1>&2
 
 # time (${buildDir}/kegAlign.sh) >> ${buildDir}/kegAlign.log 2>&1
 
 ### run the primary alignment, UCSC lastz style
 printf "running: time (${buildDir}/lastzRun.sh) >> ${buildDir}/lastzRun.log 2>&1\n" 1>&2
 
 # time (${buildDir}/lastzRun.sh) >> ${buildDir}/lastzRun.log 2>&1