411af8fc818febf61de8210a3cc05b019d9c8d2a
hiram
  Fri Oct 27 10:39:09 2023 -0700
the missing files need to be marked as an error refs #29545

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index 7efa2cd..e82de59 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -60,31 +60,31 @@
   }
   my ($gcPrefix, $accession, undef) = split('_', $asmId);
   my $accessionId = sprintf("%s_%s", $gcPrefix, $accession);
   my $accessionDir = substr($asmId, 0 ,3);
   $accessionDir .= "/" . substr($asmId, 4 ,3);
   $accessionDir .= "/" . substr($asmId, 7 ,3);
   $accessionDir .= "/" . substr($asmId, 10 ,3);
   $destDir = "/hive/data/genomes/asmHubs/$accessionDir/$accessionId";
   my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId";
   if ($gcPrefix eq "GCA") {
      $buildDir = "/hive/data/genomes/asmHubs/genbankBuild/$accessionDir/$asmId";
   }
   my $trackDb = "$buildDir/$asmId.trackDb.txt";
   if ( ! -s "${trackDb}" ) {
     printf STDERR "# %03d not built yet: %s\n", $orderIndex, $asmId;
-    printf STDERR "# missing tdb: '%s'\n", $trackDb;
+    printf STDERR "# error missing tdb: '%s'\n", $trackDb;
     next;
   }
   ++$buildDone;
   printf STDERR "# %03d symlinks %s %s\n", $buildDone, $asmId, $commonName{$asmId};
 #  printf STDERR "%s\n", $buildDir;
 #  printf STDERR "%s\n", $destDir;
   if ( ! -d "${destDir}" ) {
     `mkdir -p "${destDir}"`;
   }
   `rm -f "${destDir}/bbi"`;
   `rm -f "${destDir}/genes"`;
   `rm -f "${destDir}/ixIxx"`;
   `rm -f "${destDir}/genesGtf"`;
   `rm -f "${destDir}/liftOver"`;
   `rm -f "${destDir}/otherAligners"`;
@@ -123,37 +123,37 @@
   `ln -s "${buildDir}/genesGtf" "${destDir}/genesGtf"` if (-d "${buildDir}/genesGtf");
   `ln -s "${buildDir}/liftOver" "${destDir}/liftOver"` if (-d "${buildDir}/liftOver");
   `ln -s "${buildDir}/otherAligners" "${destDir}/otherAligners"` if (-d "${buildDir}/otherAligners");
   `ln -s ${buildDir}/html/*.html "${destDir}/html/"` if (-d "${buildDir}/html");
    my $jpgFiles =`ls ${buildDir}/html/*.jpg 2> /dev/null | wc -l`;
    chomp $jpgFiles;
    if ($jpgFiles > 0) {
     `rm -f ${destDir}/html/*.jpg`;
     `ln -s ${buildDir}/html/*.jpg "${destDir}/html/"`;
    }
 #  `ln -s ${buildDir}/html/*.png "${destDir}/genomes/${asmId}/html/"`;
   `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit" "${destDir}/${accessionId}.2bit"` if (-s "${buildDir}/trackData/addMask/${asmId}.masked.2bit");
    if (-s "${buildDir}/${asmId}.fa.gz") {
       `ln -s "${buildDir}/${asmId}.fa.gz" "${destDir}/${accessionId}.fa.gz"`;
    } else {
-      printf STDERR "# missing ${asmId}.fa.gz\n";
+      printf STDERR "# error missing ${asmId}.fa.gz\n";
    }
   `ln -s "${buildDir}/${asmId}.chrNames.fa.gz" "${destDir}/${accessionId}.chrNames.fa.gz"` if (-s "${buildDir}/${asmId}.chrNames.fa.gz");
    if (-s "${buildDir}/trackData/addMask/${asmId}.masked.2bit.bpt") {
       `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit.bpt" "${destDir}/${accessionId}.2bit.bpt"`;
    } else {
-      printf STDERR "# missing ${asmId}.masked.2bit.bpt\n";
+      printf STDERR "# error missing ${asmId}.masked.2bit.bpt\n";
    }
   `ln -s "${buildDir}/${asmId}.chrNames.2bit" "${destDir}/${accessionId}.chrNames.2bit"` if (-s "${buildDir}/${asmId}.chrNames.2bit");
    if (-s "${buildDir}/${accessionId}.untrans.gfidx") {
       if (-s "${buildDir}/${accessionId}.trans.gfidx") {
         `ln -s "${buildDir}/${accessionId}.untrans.gfidx" "${destDir}/${accessionId}.untrans.gfidx"`;
         `ln -s "${buildDir}/${accessionId}.trans.gfidx" "${destDir}/${accessionId}.trans.gfidx"`;
       }
    }
   `ln -s "${buildDir}/${asmId}.agp.gz" "${destDir}/${accessionId}.agp.gz"` if (-s "${buildDir}/${asmId}.agp.gz");
   `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/${accessionId}.chrom.sizes.txt"` if (-s "${buildDir}/${asmId}.chrom.sizes");
   `ln -s "${buildDir}/${asmId}.chromAlias.txt" "${destDir}/${accessionId}.chromAlias.txt"` if (-s "${buildDir}/${asmId}.chromAlias.txt");
   `ln -s "${buildDir}/${asmId}.chromAlias.bb" "${destDir}/${accessionId}.chromAlias.bb"` if (-s "${buildDir}/${asmId}.chromAlias.bb");
    `ln -s "${buildDir}/${asmId}.rmsk.customLib.fa.gz" "${destDir}/${accessionId}.rmsk.customLib.fa.gz"` if (-s "${buildDir}/${asmId}.rmsk.customLib.fa.gz");
   `ln -s "${buildDir}/${asmId}.repeatMasker.out.gz" "${destDir}/${accessionId}.repeatMasker.out.gz"` if (-s "${buildDir}/${asmId}.repeatMasker.out.gz");
   `ln -s "${buildDir}/${asmId}.repeatMasker.version.txt" "${destDir}/${accessionId}.repeatMasker.version.txt"` if (-s "${buildDir}/${asmId}.repeatMasker.version.txt");