ab2031dab96a23d652266a19f0fe12992304bd84
hiram
  Thu Feb 6 16:53:56 2020 -0800
warn only for liftUp not error out duplicates cause missing refs #23891

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 6132439..0b27f9a 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1441,31 +1441,31 @@
 }
 
 if [ \$gffFile -nt \$asmId.ncbiGene.bb ]; then
   (gff3ToGenePred -warnAndContinue -useName \\
     -attrsOut=\$asmId.geneAttrs.ncbi.txt \$gffFile stdout \\
       2>> \$asmId.ncbiGene.log.txt || true) | genePredFilter stdin stdout \\
         | gzip -c > \$asmId.ncbiGene.genePred.gz
   genePredCheck \$asmId.ncbiGene.genePred.gz
   export howMany=`genePredCheck \$asmId.ncbiGene.genePred.gz 2>&1 | grep "^checked" | awk '{print \$2}'`
   if [ "\${howMany}" -eq 0 ]; then
      printf "# ncbiGene: no gene definitions found in \$gffFile\n";
      cleanUp
      exit 0
   fi
   liftUp -extGenePred -type=.gp stdout \\
-      ../../sequence/\$asmId.ncbiToUcsc.lift error \\
+      ../../sequence/\$asmId.ncbiToUcsc.lift warn \\
        \$asmId.ncbiGene.genePred.gz | gzip -c \\
           > \$asmId.ncbiGene.ucsc.genePred.gz
   ~/kent/src/hg/utils/automation/gpToIx.pl \$asmId.ncbiGene.ucsc.genePred.gz \\
     | sort -u > \$asmId.ncbiGene.ix.txt
   ixIxx \$asmId.ncbiGene.ix.txt \$asmId.ncbiGene.ix \$asmId.ncbiGene.ixx
   rm -f \$asmId.ncbiGene.ix.txt
   genePredToBigGenePred \$asmId.ncbiGene.ucsc.genePred.gz stdout \\
       | sort -k1,1 -k2,2n > \$asmId.ncbiGene.bed
   (bedToBigBed -type=bed12+8 -tab -as=\$HOME/kent/src/hg/lib/bigGenePred.as \\
       -extraIndex=name \$asmId.ncbiGene.bed \\
         ../../\$asmId.chrom.sizes \$asmId.ncbiGene.bb || true)
   if [ ! -s "\$asmId.ncbiGene.bb" ]; then
     printf "# ncbiGene: failing bedToBigBed\\n" 1>&2
     exit 255
   fi
@@ -1580,31 +1580,31 @@
 } # doXenoRefGene
 
 #########################################################################
 # * step: trackDb [workhorse]
 sub doTrackDb {
   my $runDir = "$buildDir";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "construct asmId.trackDb.txt file";
   my $bossScript = newBash HgRemoteScript("$runDir/doTrackDb.bash",
                     $workhorse, $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 export asmId=$asmId
 
-\$HOME/kent/src/hg/utils/automation/doHubTrackDb.sh \$asmId $runDir \\
+\$HOME/kent/src/hg/utils/automation/asmHubTrackDb.sh \$asmId $runDir \\
    > \$asmId.trackDb.txt
 
 _EOF_
   );
   $bossScript->execute();
 } # trackDb
 
 #########################################################################
 # * step: cleanup [fileServer]
 sub doCleanup {
   my $runDir = "$buildDir";
   my $whatItDoes = "clean up or compresses intermediate files.";
   my $bossScript = newBash HgRemoteScript("$runDir/doCleanup.bash", $fileServer,
 				      $runDir, $whatItDoes);
   $bossScript->add(<<_EOF_