083fc14e534ca67e2355bab5b3e8f399bb0dc1f4
hiram
  Wed May 21 12:22:52 2025 -0700
beware some viral genomes will not have ix ixx files for ncbiGene track refs #34337

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index ce42347d0f1..7d098502636 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1867,31 +1867,33 @@
       \$asmId.ncbiGene.genePred.gz | gzip -c \\
         > \$asmId.ncbiGene.ucsc.genePred.gz
   ncbiGenePred="\$asmId.ncbiGene.ucsc.genePred.gz"
 _EOF_
       );
   }
   $bossScript->add(<<_EOF_
   genePredToBed -tab -fillSpace \$ncbiGenePred stdout \\
     | bedToExons stdin stdout | bedSingleCover.pl stdin > \$asmId.exons.bed
   export baseCount=`awk '{sum+=\$3-\$2}END{printf "%d", sum}' \$asmId.exons.bed`
   export asmSizeNoGaps=`grep sequences ../../\$asmId.faSize.txt | awk '{print \$5}'`
   export perCent=`echo \$baseCount \$asmSizeNoGaps | awk '{printf "%.3f", 100.0*\$1/\$2}'`
   rm -f \$asmId.exons.bed
   ~/kent/src/hg/utils/automation/gpToIx.pl \$ncbiGenePred \\
     | sort -u > \$asmId.ncbiGene.ix.txt
+  if [ -s \$asmId.ncbiGene.ix.txt ]; then
     ixIxx \$asmId.ncbiGene.ix.txt \$asmId.ncbiGene.ix \$asmId.ncbiGene.ixx
+  fi
   rm -f \$asmId.ncbiGene.ix.txt
   genePredToBigGenePred \$ncbiGenePred stdout \\
       | sort -k1,1 -k2,2n > \$asmId.ncbiGene.bed
   (bedToBigBed -type=bed12+8 -tab -as=\$HOME/kent/src/hg/lib/bigGenePred.as \\
       -extraIndex=name \$asmId.ncbiGene.bed \\
         ../../\$asmId.chrom.sizes \$asmId.ncbiGene.bb || true)
   if [ ! -s "\$asmId.ncbiGene.bb" ]; then
     printf "# ncbiGene: failing bedToBigBed\\n" 1>&2
     exit 255
   fi
   touch -r\$gffFile \$asmId.ncbiGene.bb
   bigBedInfo \$asmId.ncbiGene.bb | egrep "^itemCount:|^basesCovered:" \\
     | sed -e 's/,//g' > \$asmId.ncbiGene.stats.txt
   LC_NUMERIC=en_US /usr/bin/printf "# ncbiGene %s %'d %s %'d\\n" `cat \$asmId.ncbiGene.stats.txt` | xargs echo
   printf "%d bases of %d (%s%%) in intersection\\n" "\$baseCount" "\$asmSizeNoGaps" "\$perCent" > fb.\$asmId.ncbiGene.txt