a4984ed4a91768bac66cecaf7593bc0b7fca453f
hiram
  Mon Jan 19 14:12:05 2026 -0800
correctly recognize files in a blat directory refs #35575

diff --git src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh
index 2c6e9fafce4..eb0f3b50cd0 100755
--- src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh
+++ src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh
@@ -73,52 +73,65 @@
 fi
 
 export QueryAcc="${queryAcc^}"
 export targetQueryOverChain="${targetAcc}.${queryAcc}.over.chain.gz"
 export fbTargetQuery="../fb.${targetAcc}.quick${QueryAcc}Link.txt"
 
 if [ ! -d "${queryDir}" ]; then
    printf "ERROR: can not find queryDir: '%s'\n" "${queryDir}" 1>&2
    exit 255
 fi
 
 export axtChain="${targetDir}/lastz.${queryAcc}/axtChain"
 printf "checking: %s\n" "${axtChain}" 1>&2
 printf "checking: %s\n" "${targetQueryOverChain}" 1>&2
 if [ ! -d "${axtChain}" ]; then
-   axtChain="`ls -d ${targetDir}/blat.${queryAcc}.* | tail -1`"
+   printf "checking ${targetDir}/blastz.${queryAcc}/axtChain\n" 1>&2
+   ls -d ${targetDir}/blastz.${queryAcc}/axtChain || true
+   axtChain="`ls -d ${targetDir}/blastz.${queryAcc}/axtChain || true | tail -1`"
+   if [ -d "${axtChain}" ]; then
+       targetQueryOverChain="${axtChain}/${targetAcc}.${queryAcc}.over.chain.gz"
+       fbTargetQuery="fb.${targetAcc}.quick${QueryAcc}Link.txt"
+       quickLinkSrc="${axtChain}/${targetAcc}.${queryAcc}"
+   else
+       printf "checking ${targetDir}/blat.${queryAcc}.*\n" 1>&2
+       ls -d ${targetDir}/blat.${queryAcc}.* || true
+       axtChain="`ls -d ${targetDir}/blat.${queryAcc}.* || true | tail -1`"
        if [ -d "${axtChain}" ]; then
          targetQueryOverChain="${axtChain}/${targetAcc}To${QueryAcc}.over.chain.gz"
          fbTargetQuery="fb.${targetAcc}.quick${QueryAcc}Link.txt"
          quickLinkSrc="${axtChain}/${targetAcc}.${queryAcc}"
          if [ ! -s "${targetQueryOverChain}" ]; then
            printf "ERROR: can not find target.query.over.chain:\n%s\n" "${targetQueryOverChain}"
            exit 255
          fi
        else
          printf "ERROR: can not find axtChain: '%s'\n" "${axtChain}" 1>&2
          exit 255
        fi
    fi
+fi
 
 cd "${axtChain}"
 
+# rm -f "${fbTargetQuery}"
 if [ -s "${fbTargetQuery}" ]; then
   printf "DONE: ${target} ${query} %s\n" "`cat ${fbTargetQuery}`" 1>&2
   exit 0
 fi
 
+# rm -f "${quickLinkPath}.bb"
 if [ -s "${quickLinkPath}.bb" ]; then
   printf "symLink exists: ${quickLinkPath}.bb\n" 1>&2
   exit 0
 fi
 
 if [ ! -s "${targetQueryOverChain}" ]; then
   printf "ERROR: can not find target.query.over.chain:\n%s\n" "${targetQueryOverChain}"
   exit 255
 fi
 
 printf "working: %s\n" "${axtChain}" 1>&2
 printf "%s\n" "${targetSizes}" 1>&2
 printf "%s\n" "${querySizes}" 1>&2
 printf "%s\n" "${targetQueryOverChain}" 1>&2
 printf "%s\n" "${fbTargetQuery}" 1>&2