3b5ca881b4a3a665d84a60f38974090888f08931
hiram
  Wed Dec 8 15:04:40 2021 -0800
avoid building blat indexes for genomes that are too large no redmine

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index c87a945..9567309 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1403,38 +1403,43 @@
   my $src2BitToMask = "../repeatMasker/$asmId.rmsk.2bit";
   if ($noRmsk || ($wmMasked > $rmMasked)) {
     $src2BitToMask = "../windowMasker/$asmId.cleanWMSdust.2bit";
   }
 
   $bossScript->add(<<_EOF_
 export asmId=$asmId
 export accessionId=`echo \$asmId | cut -d'_' -f1-2`
 
 if [ ../simpleRepeat/trfMask.bed.gz -nt \$asmId.masked.faSize.txt ]; then
   twoBitMask $src2BitToMask -type=.bed \\
      -add ../simpleRepeat/trfMask.bed.gz \$asmId.masked.2bit
   twoBitToFa \$asmId.masked.2bit stdout | faSize stdin > \$asmId.masked.faSize.txt
   touch -r \$asmId.masked.2bit \$asmId.masked.faSize.txt
   cp -p \$asmId.masked.faSize.txt ../../\$asmId.faSize.txt
+  size=`grep -w bases \$asmId.masked.faSize.txt | cut -d' ' -f1`
+  if [ \$size -lt 4294967297 ]; then
     ln \$asmId.masked.2bit \$accessionId.2bit
     gfServer -trans index ../../\$accessionId.trans.gfidx \$accessionId.2bit &
     gfServer -stepSize=5 index ../../\$accessionId.untrans.gfidx \$accessionId.2bit
     wait
     rm \$accessionId.2bit
     touch -r \$asmId.masked.2bit ../../\$accessionId.trans.gfidx
     touch -r \$asmId.masked.2bit ../../\$accessionId.untrans.gfidx
   else
+    printf "# genome \$asmId too large at \$size to make blat indexes\\n" 1>&2
+  fi
+else
   printf "# addMask step previously completed\\n" 1>&2
   exit 0
 fi
 _EOF_
   );
 
   $bossScript->execute();
 } # addMask
 
 #########################################################################
 # * step: windowMasker [workhorse]
 sub doWindowMasker {
   my $runDir = "$buildDir/trackData/windowMasker";
 
   &HgAutomate::mustMkdir($runDir);