a8a20738a644d24872835b8ef5e0d9608bdd3bdf
hiram
  Wed Dec 1 15:40:57 2021 -0800
do not fail on empty genePred for ncbiGene no redmine

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index f8434ef..77376e3 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1614,31 +1614,31 @@
      }
   }
   if (! -s "$buildDir/$asmId.faSize.txt") {
     &HgAutomate::verbose(1, "# step ncbiGene: can not find faSize.txt at:\n#  $buildDir/$asmId.faSize.txt\n");
     exit 255;
   }
 
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "translate NCBI GFF3 gene definitions into a track";
   my $bossScript = newBash HgRemoteScript("$runDir/doNcbiGene.bash",
                     $workhorse, $runDir, $whatItDoes);
 
   my $dupList = "";
   if ( -s "${buildDir}/download/${asmId}.remove.dups.list" ) {
-    $dupList = " | grep -v -f \"${buildDir}/download/${asmId}.remove.dups.list\" ";
+    $dupList = " | grep -v -f \"${buildDir}/download/${asmId}.remove.dups.list\"  || true";
   }
 
   $bossScript->add(<<_EOF_
 export asmId=$asmId
 export gffFile=$gffFile
 
 function cleanUp() {
   rm -f \$asmId.ncbiGene.genePred.gz \$asmId.ncbiGene.genePred
   rm -f \$asmId.geneAttrs.ncbi.txt
 }
 
 if [ \$gffFile -nt \$asmId.ncbiGene.bb ]; then
   (gff3ToGenePred -warnAndContinue -useName \\
     -attrsOut=\$asmId.geneAttrs.ncbi.txt \$gffFile stdout \\
       2>> \$asmId.ncbiGene.log.txt || true) | genePredFilter \\