8149f2d63d04238813b626ab194b45eeaa91e32f
hiram
  Tue Sep 29 15:20:22 2026 -0700
fixup swap directory recognition refs #34360

diff --git src/hg/utils/automation/asmHubTrackDb.sh src/hg/utils/automation/asmHubTrackDb.sh
index 7c3654111c1..0329c8cf85e 100755
--- src/hg/utils/automation/asmHubTrackDb.sh
+++ src/hg/utils/automation/asmHubTrackDb.sh
@@ -1099,36 +1099,40 @@
     export oOrganism=`basename "${lastzDir}" | sed -e 's/lastz.//;'`
     # single chainNet here, no need for a composite track, does the symLinks too
     $scriptDir/asmHubChainNetTrackDb.sh $asmId $buildDir
     $scriptDir/asmHubChainNet.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab $oOrganism > $buildDir/html/$asmId.chainNet.html
   else
 printf "composite chainNet\n" 1>&2
     # multiple chainNets here, create composite track, does the symLinks too
     $scriptDir/asmHubChainNetTrackDb.pl $buildDir
     $scriptDir/asmHubChainNetComposite.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab > $buildDir/html/$asmId.chainNet.html
   fi
 fi
 
 ###################################################################
 # check for miniMap2/chain/net available
 
-export mm2=`ls -d ${buildDir}/trackData/miniMap2.* 2> /dev/null | wc -l`
+# a -swap run's default swapDir is itself named 'miniMap2.<otherDb>.swap',
+# which also matches this glob alongside its own dateless symlink
+# 'miniMap2.<otherDb>' -- exclude those real *.swap work directories so
+# each query genome is only counted/processed once.
+export mm2=`ls -d ${buildDir}/trackData/miniMap2.* 2> /dev/null | grep -v '\.swap$' | wc -l`
 
 if [ "${mm2}" -gt 0 ]; then
   if [ "${mm2}" -eq 1 ]; then
 printf "single miniMap2 chainNet\n" 1>&2
-    export miniMap2Dir=`ls -d ${buildDir}/trackData/miniMap2.*`
+    export miniMap2Dir=`ls -d ${buildDir}/trackData/miniMap2.* | grep -v '\.swap$'`
     export oOrganism=`basename "${miniMap2Dir}" | sed -e 's/miniMap2.//;'`
     # single chainNet here, no need for a composite track, does the symLinks too
     $scriptDir/asmHubMiniMap2ChainNetTrackDb.sh $asmId $buildDir
     $scriptDir/asmHubMiniMap2ChainNet.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab $oOrganism > $buildDir/html/$asmId.miniMap2ChainNet.html
   else
 printf "composite miniMap2 chainNet\n" 1>&2
     # multiple chainNets here, create composite track, does the symLinks too
     $scriptDir/asmHubMiniMap2ChainNetTrackDb.pl $buildDir
     $scriptDir/asmHubMiniMap2ChainNetComposite.pl $asmId $ncbiAsmId $buildDir/html/$asmId.names.tab > $buildDir/html/$asmId.miniMap2ChainNet.html
   fi
 fi
 
 ###################################################################
 # crisprAll track