2616623a638ac5f6606049570e44f0ea040f0353
hiram
  Thu May 9 08:19:37 2024 -0700
not all liftOver chains have nets

diff --git src/hg/utils/automation/asmHubChainNetTrackDb.sh src/hg/utils/automation/asmHubChainNetTrackDb.sh
index 2bc48fc..28f0dbc 100755
--- src/hg/utils/automation/asmHubChainNetTrackDb.sh
+++ src/hg/utils/automation/asmHubChainNetTrackDb.sh
@@ -85,32 +85,34 @@
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.synNet.bb $buildDir/bbi/${asmId}.$otherDb.synNet.bb
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.synNet.summary.bb $buildDir/bbi/${asmId}.$otherDb.synNet.summary.bb
   fi
   if [ -s "$buildDir/trackData/$lastzDir/axtChain/chainRBest${OtherDb}.bb" ]; then
     ln -s ../trackData/$lastzDir/axtChain/chainRBest${OtherDb}.bb $buildDir/bbi/${asmId}.chainRBest$OtherDb.bb
     ln -s ../trackData/$lastzDir/axtChain/chainRBest${OtherDb}Link.bb $buildDir/bbi/${asmId}.chainRBest${OtherDb}Link.bb
   fi
   if [ -s "$buildDir/trackData/$lastzDir/bigMaf/$accessionId.$otherDb.rbestNet.bb" ]; then
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.rbestNet.bb $buildDir/bbi/${asmId}.$otherDb.rbestNet.bb
     ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.rbestNet.summary.bb $buildDir/bbi/${asmId}.$otherDb.rbestNet.summary.bb
   fi
   if [ -s "$buildDir/trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}.bb" ]; then
 printf "# making chainLiftOver${OtherDb}.bb\n" 1>&2
     ln -s ../trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}.bb $buildDir/bbi/${asmId}.chainLiftOver$OtherDb.bb
     ln -s ../trackData/$lastzDir/axtChain/chainLiftOver${OtherDb}Link.bb $buildDir/bbi/${asmId}.chainLiftOver${OtherDb}Link.bb
+    if [ -s "$buildDir/trackData/$lastzDir/bigMaf/${accessionId}.${otherDb}.liftOverNet.bb" ]; then
       ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.liftOverNet.bb $buildDir/bbi/${asmId}.$otherDb.liftOverNet.bb
       ln -s ../trackData/$lastzDir/bigMaf/$accessionId.$otherDb.liftOverNet.summary.bb $buildDir/bbi/${asmId}.$otherDb.liftOverNet.summary.bb
+    fi
   else
 printf "# there is NO chainLiftOver${OtherDb}.bb\n" 1>&2
   fi
 
   otherPrefix=`echo $otherDb | cut -c1-2`
   if [ "${otherPrefix}" = "GC" ]; then
     sciName=`grep -i 'organism name:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*organism name: *//i; s/ *(.*//;'`
     organism=`grep -i 'organism name:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*organism name: *.*(//i; s/).*//;'`
     taxId=`grep -i 'taxid:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*taxid: *//i;'`
     o_date=`grep -i 'date:' ${asmReport} | head -1 | tr -d "\r" | sed -e 's/.*date: *//i;'`
     matrix=""
     linGap=""
     minScore=""
   else
     organism=`hgsql -N -e "select organism from dbDb where name=\"$otherDb\"" hgcentraltest`