03456e3b8643743836b3c76c667ddd8ed6d4af82
hiram
  Thu Nov 26 22:26:55 2020 -0800
fixup chromAlias build for NCBI named assemblies and have duplicates refs #24396

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index b021e16..7ece3ca 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -981,32 +981,32 @@
   &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=$asmId
 
 \$HOME/kent/src/hg/utils/automation/asmHubChromAlias.pl \\
     \${asmId} | sort > \${asmId}.chromAlias.txt
 # verify each sequence name has an alias
 export sizeCount=`cat ../../\${asmId}.chrom.sizes | wc -l`
 export aliasCount=`grep -v "^#" \${asmId}.chromAlias.txt | wc -l`
-if [ "\${sizeCount}" -ne "\${aliasCount}" ]; then
-  printf "ERROR: chromAlias: incorrect number of aliases %d != %d\\n" "\${sizeCount}" "\${aliasCount}" 1>&2
+if [ "\${sizeCount}" -gt "\${aliasCount}" ]; then
+  printf "ERROR: chromAlias: incorrect number of aliases chromSizes %d > %d aliasCount\\n" "\${sizeCount}" "\${aliasCount}" 1>&2
   exit 255
 fi
 
 exit 0
 
 _EOF_
   );
   $bossScript->execute();
 } # chromAlias
 
 #########################################################################
 # * step: gatewayPage [workhorse]
 sub doGatewayPage {
   if ($asmHubName eq "n/a") {
     printf STDERR "ERROR: step gatewayPage needs argument -asmHubName <name>\n";