e3c90a0c1514cc8f4e0bf17618fd2d2d06e235ef
hiram
  Mon May 2 10:16:21 2022 -0700
clean up loose ends no redmine

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 4a70f89..dfbcc0b 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1452,30 +1452,33 @@
   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
   bptForTwoBit \$asmId.masked.2bit \$asmId.masked.2bit.bpt
   touch -r \$asmId.masked.2bit \$asmId.masked.2bit.bpt
+  twoBitToFa \$asmId.masked.2bit stdout | gzip -c > \$asmId.fa.gz
+  touch -r \$asmId.masked.2bit \$asmId.fa.gz
+  cp -p \$asmId.fa.gz ../../\$asmId.fa.gz
   cp -p \$asmId.masked.faSize.txt ../../\$asmId.faSize.txt
   cp -p \$asmId.masked.2bit.bpt ../../\$asmId.2bit.bpt
   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