5e98a4b579ae9b7efbcc20c0314b7b51e88b7caf
hiram
  Mon May 29 12:13:19 2023 -0700
do not look for a database when it is an assembly hub (hs1) refs #31342

diff --git src/hg/utils/automation/doNcbiRefSeq.pl src/hg/utils/automation/doNcbiRefSeq.pl
index ed20aed..08e2ef7 100755
--- src/hg/utils/automation/doNcbiRefSeq.pl
+++ src/hg/utils/automation/doNcbiRefSeq.pl
@@ -984,31 +984,33 @@
   die "ERROR: can not find /hive/data/genomes/$db/bed/idKeys/$db.idKeys.txt\n\t  need to run doIdKeys.pl for $db before this procedure.";
 }
 
 # Force debug and verbose until this is looking pretty solid:
 # $opt_debug = 1;
 # $opt_verbose = 3 if ($opt_verbose < 3);
 
 # Establish what directory we will work in.
 my $date = `date +%Y-%m-%d`;
 chomp $date;
 $buildDir = $opt_buildDir ? $opt_buildDir :
   "$HgAutomate::clusterData/$db/$HgAutomate::trackBuild/ncbiRefSeq.$date";
 
 # may be working on a 2bit file that does not have a database browser
 $dbExists = 0;
+if (! $opt_assemblyHub) {
   $dbExists = 1 if (&HgAutomate::databaseExists($dbHost, $db));
+}
 
 # Do everything.
 $stepper->execute();
 
 $secondsEnd = `date "+%s"`;
 chomp $secondsEnd;
 my $elapsedSeconds = $secondsEnd - $secondsStart;
 my $elapsedMinutes = int($elapsedSeconds/60);
 $elapsedSeconds -= $elapsedMinutes * 60;
 
 # Tell the user anything they should know.
 my $stopStep = $stepper->getStopStep();
 my $upThrough = ($stopStep eq 'cleanup') ? "" :
   "  (through the '$stopStep' step)";