decbe499b06103596243d27e31a49cff37f5511f
hiram
  Tue Aug 2 12:40:35 2022 -0700
correctly zcat the correct file sorted.fa.out.gz refs #29545

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index c03ae79..a51003a 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -183,31 +183,31 @@
   fi	#	the else clause of: if [ -z ${not_tanDups+x} ]
 fi	#	if [ "${gapOverlapCount}" -gt 0 -o "${tanDupCount}" -gt 0 ]
 
 # see if there are repeatMasker bb files
 export rmskCount=`(ls $buildDir/trackData/repeatMasker/bbi/${asmId}.rmsk.*.bb 2> /dev/null | wc -l) || true`
 export newRmsk=`(ls $buildDir/trackData/repeatMasker/${asmId}.rmsk.align.bb $buildDir/trackData/repeatMasker/${asmId}.rmsk.bb 2> /dev/null | wc -l) || true`
 
 if [ "${newRmsk}" -gt 0 -o "${rmskCount}" -gt 0 ]; then
 
 if [ ! -s "$buildDir/trackData/repeatMasker/$asmId.sorted.fa.out.gz" ]; then
   printf "ERROR: can not find trackData/repeatMasker/$asmId.sorted.fa.out.gz\n" 1>&2
   exit 255
 fi
 
 # see if there are actually rmsk items in the track, this has to be > 3
-export rmskItemCount=`zcat $buildDir/trackData/repeatMasker/$asmId.sorted.fa.out.g | head | wc -l`
+export rmskItemCount=`zcat $buildDir/trackData/repeatMasker/$asmId.sorted.fa.out.gz | head | wc -l`
 
 # clean up garbage from previous errors here
 if [ "${rmskItemCount}" -lt 4 ]; then
   rm -f $buildDir/$asmId.repeatMasker.out.gz
   rm -f "$buildDir/${asmId}.repeatMasker.version.txt"
   rm -f $buildDir/bbi/${asmId}.rmsk.align.bb
   rm -f $buildDir/bbi/${asmId}.rmsk.bb
   rm -f $buildDir/${asmId}.fa.align.tsv.gz
   rm -f $buildDir/${asmId}.fa.join.tsv.gz
 else
 
 rm -f $buildDir/$asmId.repeatMasker.out.gz
 ln -s trackData/repeatMasker/$asmId.sorted.fa.out.gz $buildDir/$asmId.repeatMasker.out.gz
 if [ -s "$buildDir/trackData/repeatMasker/versionInfo.txt" ]; then
    rm -f "$buildDir/${asmId}.repeatMasker.version.txt"