9c779856e423e2f2030758080f93d8e1448b95b1
hiram
  Fri Oct 27 10:44:05 2023 -0700
do not need to do twoBitToFa twice in addMask, once is enough refs #29545

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 65f2320..22f5794 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1542,36 +1542,36 @@
 export asmId=$defaultName
 export src2Bit=$src2BitToMask
 export accessionId=$accessionId
 
 # if simple repeat has a result, add it, otherwise no add
 if [ -s ../simpleRepeat/trfMask.bed.gz ]; then
   if [ ../simpleRepeat/trfMask.bed.gz -nt \$asmId.masked.faSize.txt ]; then
     twoBitMask \$src2Bit -type=.bed \\
        -add ../simpleRepeat/trfMask.bed.gz \$asmId.masked.2bit
   fi
 else
   cp -p \$src2Bit \$asmId.masked.2bit
 fi
 
 if [ \$asmId.masked.2bit -nt \$asmId.masked.faSize.txt ]; then
-  twoBitToFa \$asmId.masked.2bit stdout | faSize stdin > \$asmId.masked.faSize.txt
+  twoBitToFa \$asmId.masked.2bit stdout | gzip -c > \$asmId.fa.gz
+  touch -r \$asmId.masked.2bit \$asmId.fa.gz
+  faSize \$asmId.fa.gz > \$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