e1625b2bf30df1d1f9385bc79fc2cbd45a05d511
hiram
  Fri May 1 12:41:32 2026 -0700
explicit path names to allow these scripts to work on cron jobs refs #31811

diff --git src/hg/utils/automation/asmHubRepeatMasker.sh src/hg/utils/automation/asmHubRepeatMasker.sh
index 8e2f0c3274f..5eed4a94ed7 100755
--- src/hg/utils/automation/asmHubRepeatMasker.sh
+++ src/hg/utils/automation/asmHubRepeatMasker.sh
@@ -126,31 +126,31 @@
     fi
     dateStamp=`date "+%FT%T %s"`
     printf "# %s checking ls rmskClass/*.tab | egrep -v \"/SIN|/LIN|/LT|/DN|/Simple|/Low_complexity|/Satellit|RNA.tab\"\n" "${dateStamp}"
     otherCount=`(ls rmskClass/*.tab 2> /dev/null || true) | (egrep -v "/SIN|/LIN|/LT|/DN|/Simple|/Low_complexity|/Satellit|RNA.tab" || true) | wc -l`
     if [ "${otherCount}" -gt 0 ]; then
       dateStamp=`date "+%FT%T %s"`
       printf "# %s bedToBigBed on: " "${dateStamp}"
       ls rmskClass/*.tab | egrep -v "/SIN|/LIN|/LT|/DN|/Simple|/Low_complexity|/Satellit|RNA.tab" | xargs echo | sed -e 's#rmskClass/##g;'
       $HOME/kent/src/hg/utils/automation/rmskBed6+10.pl `ls rmskClass/*.tab | egrep -v "/SIN|/LIN|/LT|/DN|/Simple|/Low_complexity|/Satellit|RNA.tab" | sed -e 's/^/"/; s/$/"/;'|xargs echo` \
           | sort -k1,1 -k2,2n > classBed/${asmId}.rmsk.Other.bed
       bedToBigBed -tab -type=bed6+10 -as=$HOME/kent/src/hg/lib/rmskBed6+10.as \
         classBed/${asmId}.rmsk.Other.bed "${chrSizes}" \
           bbi/${asmId}.rmsk.Other.bb
     fi
 
-    export bbiCount=`for F in bbi/*.rmsk.*.bb; do bigBedInfo $F | grep itemCount; done | awk '{print $NF}' | sed -e 's/,//g' | ave stdin | grep total | awk '{print $2}' | sed -e 's/.000000//'`
+    export bbiCount=`for F in bbi/*.rmsk.*.bb; do bigBedInfo $F | grep itemCount; done | awk '{print $NF}' | sed -e 's/,//g' | /cluster/bin/x86_64/ave stdin | grep total | awk '{print $2}' | sed -e 's/.000000//'`
 
     export firstTabCount=`cat ${asmId}.rmsk.tab | wc -l`
     export splitTabCount=`cat rmskClass/*.tab | wc -l`
 
     if [ "$firstTabCount" -ne $bbiCount ]; then
        printf "%s.rmsk.tab count: %d, split class tab file count: %d, bbi class item count: %d\n" "${asmId}" $firstTabCount $splitTabCount $bbiCount 1>&2
        printf "ERROR: did not account for all items in rmsk class bbi construction\n" 1>&2
        exit 255
     fi
     wc -l classBed/*.bed > ${asmId}.rmsk.class.profile.txt
     wc -l rmskClass/*.tab >> ${asmId}.rmsk.class.profile.txt
     rm -fr rmskClass classBed ${asmId}.rmsk.tab
   fi
   rm -f "${rmOutTmp}"
 else