0f9627d32b1a95d56c1078595924d387375e487d
hiram
  Tue Sep 13 14:37:39 2022 -0700
the chromAlias needs to know about the NCBI asmId refs #29811

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 4f8120d..ebd61b3 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1016,31 +1016,31 @@
 #########################################################################
 # * step: chromAlias [workhorse]
 sub doChromAlias {
   my $runDir = "$buildDir/trackData/chromAlias";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "construct asmId.chromAlias.txt for alias name recognition";
   my $bossScript = newBash HgRemoteScript("$runDir/doChromAlias.bash",
                     $workhorse, $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 export buildDir=$buildDir
 export asmId="$defaultName"
 
 \$HOME/kent/src/hg/utils/automation/asmHubChromAlias.pl \\
-    \${asmId} | sort > \${asmId}.chromAlias.txt
+    \${asmId} $asmId | sort > \${asmId}.chromAlias.txt
 
 \$HOME/kent/src/hg/utils/automation/aliasTextToBed.pl \\
   -chromSizes=\$buildDir/\$asmId.chrom.sizes \\
     -aliasText=\${asmId}.chromAlias.txt \\
       -aliasBed=\${asmId}.chromAlias.bed \\
         -aliasAs=\${asmId}.chromAlias.as \\
         -aliasBigBed=\${asmId}.chromAlias.bb
 
 bigBedToBed -header \${asmId}.chromAlias.bb test.chromAlias.bed
 \$HOME/kent/src/hg/utils/automation/aliasBedToCt.pl \\
   test.chromAlias.bed \${asmId}.chromAlias.bb .
 
 # verify each sequence name has an alias
 export sizeCount=`grep -c . ../../\${asmId}.chrom.sizes`
 export aliasCount=`grep -c -v "^#" \${asmId}.chromAlias.txt`