db6d277aafb53f3f3d5bad08d3821ae98a29a045
hiram
  Wed Apr 29 14:29:34 2020 -0700
fix use of verbose() in ncbiGene refs #23734

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 41b0111..bc49a4b 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1471,50 +1471,50 @@
     -chromSizes=$buildDir/\$asmId.chrom.sizes \$asmId
 else
   printf "# cpgIslands masked previously completed\\n" 1>&2
   exit 0
 fi
 _EOF_
   );
   $bossScript->execute();
 } # sub doCpgIslands
 
 #########################################################################
 # * step: ncbiGene [workhorse]
 sub doNcbiGene {
   my $gffFile = "$assemblySource/${asmId}_genomic.gff.gz";
   if ( ! -s "${gffFile}" ) {
-    &HgAutomate::verbose(1, "# step ncbiGene: no gff file found at:\n#  %s\n", $gffFile);
+    &HgAutomate::verbose(1, "# step ncbiGene: no gff file found at:\n#  $gffFile\n");
     return;
   }
   if ( ! -s "$buildDir/sequence/$asmId.ncbiToUcsc.lift" ) {
     &HgAutomate::verbose(1, "# ERROR: ncbiGene: can not find $buildDir/sequence/$asmId.ncbiToUcsc.lift\n");
     exit 255;
   }
   my $runDir = "$buildDir/trackData/ncbiGene";
   if (-d "${runDir}" ) {
      if (! -s "$runDir/$asmId.ncbiGene.bb") {
        &HgAutomate::verbose(1,
        "WARNING ncbiGene step may already be running, but not completed ?\n");
        return;
      } elsif (! needsUpdate("$gffFile", "$runDir/$asmId.ncbiGene.bb")) {
        &HgAutomate::verbose(1, "# ncbiGene step previously completed\n");
        return;
      }
   }
   if (! -s "$buildDir/$asmId.faSize.txt") {
-    &HgAutomate::verbose(1, "# step ncbiGene: can not find faSize.txt at:\n#  %s\n", "$buildDir/$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);
 
   $bossScript->add(<<_EOF_
 export asmId=$asmId
 export gffFile=$gffFile
 
 function cleanUp() {
   rm -f \$asmId.ncbiGene.genePred.gz \$asmId.ncbiGene.genePred