e828b8c24fd241d8a974cc4d5bbccbebc9de89de
hiram
  Thu Jan 23 15:10:59 2020 -0800
use warnOnly on the gff conversion in ncbiRefSeq track refs #24748

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 8a649b9..8a1f131 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1486,31 +1486,31 @@
 
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "run NCBI RefSeq gene procedures";
   my $bossScript = newBash HgRemoteScript("$runDir/doNcbiRefSeq.bash",
                     $workhorse, $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 export asmId="$asmId"
 export buildDir="$buildDir"
 export liftFile="\$buildDir/sequence/\$asmId.ncbiToUcsc.lift"
 export target2bit="\$buildDir/\$asmId.2bit"
 
 if [ $buildDir/\$asmId.2bit -nt \$asmId.ncbiRefSeq.bb ]; then
 
-~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -buildDir=`pwd` \\
+~/kent/src/hg/utils/automation/doNcbiRefSeq.pl -toGpWarnOnly -buildDir=`pwd` \\
       -bigClusterHub=$bigClusterHub -dbHost=$dbHost \\
       -liftFile="\$liftFile" \\
       -target2bit="\$target2bit" \\
       -stop=load -fileServer=$fileServer -smallClusterHub=$smallClusterHub -workhorse=$workhorse \\
       $genbankRefseq $subGroup $species \\
       \$asmId \$asmId
 else
   printf "# ncbiRefSeq previously completed\\n" 1>&2
 fi
 _EOF_
   );
   $bossScript->execute();
 } # ncbiRefSeq
 
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