d40445e1154b5384876ca6b69bd069518762ea6d
hiram
  Thu Sep 10 21:52:57 2026 -0700
working with new simpleRepeat output refs #38321

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 785329f0c58..883daa89349 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1354,30 +1354,35 @@
   }
 
   $bossScript->add(<<_EOF_
 export asmId=$defaultName
 export buildDir=$buildDir
 
 if [ \$buildDir/\$asmId.2bit -nt trfMask.bed.gz ]; then
   doSimpleRepeat.pl -stop=filter -buildDir=`pwd` \\
     -unmaskedSeq=\$buildDir/\$asmId.2bit \\
       -trf409=6 -dbHost=$dbHost -smallClusterHub=$trfClusterHub \\
         -workhorse=$workhorse \$asmId
   doSimpleRepeat.pl -buildDir=`pwd` \\
     -continue=cleanup -stop=cleanup -unmaskedSeq=\$buildDir/\$asmId.2bit \\
       -trf409=6 -dbHost=$dbHost -smallClusterHub=$trfClusterHub \\
         -workhorse=$workhorse \$asmId
+  if [ -s simpleRepeat.merge.bed ]; then
+    gzip simpleRepeat.merge.bed &
+  else
+    rm -f simpleRepeat.merge.bed
+  fi
   if [ -s simpleRepeat.bed ]; then
     gzip simpleRepeat.bed &
   else
     rm -f simpleRepeat.bed
   fi
   if [ -s trfMask.bed ]; then
     gzip trfMask.bed &
   fi
   wait
 fi
 _EOF_
   );
   $bossScript->execute();
 } # simpleRepeat