4f90338a4d065f90adf1de2d88ebf66be91efca8
hiram
  Thu Apr 7 13:23:57 2022 -0700
better cleanup no redmine

diff --git src/hg/utils/automation/doAugustus.pl src/hg/utils/automation/doAugustus.pl
index 7f277bf..d9face2 100755
--- src/hg/utils/automation/doAugustus.pl
+++ src/hg/utils/automation/doAugustus.pl
@@ -365,30 +365,31 @@
 sub doCleanup {
   my $runDir = $buildDir;
 
   if (-e "$runDir/augustus.gtf.gz" ) {
     die "doCleanup: looks like this was run successfully already\n" .
       "(augustus.gtf.gz exists).  Investigate the run directory:\n" .
 	" $runDir/\n";
   }
   my $whatItDoes = "It cleans up or compresses intermediate files.";
   my $bossScript = newBash HgRemoteScript("$runDir/cleanup.bash", $workhorse,
 				      $runDir, $whatItDoes);
   $bossScript->add(<<_EOF_
 export db="$db"
 rm -fr $buildDir/fasta
 rm -fr $buildDir/run.augustus/err/
+rm -fr $buildDir/run.augustus/gtf/
 rm -f $buildDir/run.augustus/batch.bak
 rm -fr $buildDir/run.augustus/augErr
 rm -f $buildDir/\$db.augustus.bgp
 gzip $buildDir/\$db.augustus.gtf
 gzip $buildDir/\$db.augustus.gp
 gzip $buildDir/\$db.augustusGene.rna.fa
 gzip $buildDir/\$db.augustusGene.faa
 _EOF_
   );
   $bossScript->execute();
 } # doCleanup
 
 #########################################################################
 # main