bca05e23f34ba02d4048494770e9ccaa2f178cd5
hiram
  Thu May 28 12:02:00 2020 -0700
due to removed duplicates from NCBI assemblies, warn and drop contigs not in the UCSC assembly refs #23734

diff --git src/hg/utils/automation/doRepeatMasker.pl src/hg/utils/automation/doRepeatMasker.pl
index ea129c4..fbd1b125 100755
--- src/hg/utils/automation/doRepeatMasker.pl
+++ src/hg/utils/automation/doRepeatMasker.pl
@@ -431,31 +431,31 @@
 "liftUp (with no lift specs) is used to concatenate .out files because it\n" .
 "uniquifies (per input file) the .out IDs which can then be used to join\n" .
 "fragmented repeats in the Nested Repeats track.";
   my $fileServer = &HgAutomate::chooseFileServer($runDir);
   my $bossScript = newBash HgRemoteScript("$runDir/doCat.bash", $fileServer,
 				      $runDir, $whatItDoes);
 
   $bossScript->add("# Debug mode -- don't know the real number of levels\n")
     if ($opt_debug);
 
   if ($ncbiRmsk) {
     my $zippedSource = 0;	# asssume not a gz zipped file
     $zippedSource = 1 if ($ncbiRmsk =~ m/.gz$/);
     my $liftOpts = "";
     if (-s "${liftSpec}" ) {
-      $liftOpts = "| liftUp -type=.out stdout $liftSpec carry stdin";
+      $liftOpts = "| liftUp -type=.out stdout $liftSpec warn stdin";
     }
     $bossScript->add(<<_EOF_
 export db="${db}"
 export ncbiRmOutFile="${ncbiRmsk}"
 cat /dev/null > "\${db}.sorted.fa.out"
 _EOF_
     );
     if ($zippedSource) {
     $bossScript->add(<<_EOF_
 zcat "\${ncbiRmOutFile}" | tail -n +4 | sort -k5,5 -k6,6n $liftOpts >> "\${db}.sorted.fa.out"
 _EOF_
     );
     } else {
     $bossScript->add(<<_EOF_
 tail -n +4 "\${ncbiRmOutFile}" sort -k5,5 -k6,6n $liftOpts >> "\${db}.sorted.fa.out"