cf6d10c6d02bad7a97ec933fff5acd453272ffe9
galt
  Wed Nov 2 22:59:55 2022 -0700
fixed minor typo in this script where "z" was accidentally inserted in front of something that should just be cat since it is not a gzipped file.

diff --git src/hg/utils/automation/doNcbiRefSeq.pl src/hg/utils/automation/doNcbiRefSeq.pl
index 431f021..ed20aed 100755
--- src/hg/utils/automation/doNcbiRefSeq.pl
+++ src/hg/utils/automation/doNcbiRefSeq.pl
@@ -886,31 +886,31 @@
     | grep -Fwf \$db.noRna.available.list \\
       | grep chrM > missingChrMFa.psl
   if [ -s missingChrMFa.psl ]; then
     pslToBed missingChrMFa.psl stdout \\
       | twoBitToFa -bed=stdin $dbTwoBit stdout >> \$db.rna.fa
   fi
 fi
 
 mkdir -p $gbdbDir
 ln -f -s `pwd`/\$db.rna.fa $gbdbDir/seqNcbiRefSeq.rna.fa
 hgLoadSeq -drop -seqTbl=seqNcbiRefSeq -extFileTbl=extNcbiRefSeq \$db $gbdbDir/seqNcbiRefSeq.rna.fa
 
 hgLoadPsl \$db -table=ncbiRefSeqPsl process/\$asmId.\$db.psl.gz
 
 if [ -s process/\$asmId.rna.cds ]; then
-  zcat process/\$asmId.rna.cds | grep '[0-9]\\+\\.\\.[0-9]\\+' \\
+  cat process/\$asmId.rna.cds | grep '[0-9]\\+\\.\\.[0-9]\\+' \\
     | pslMismatchGapToBed -cdsFile=stdin -db=\$db -ignoreQNamePrefix=X \\
       process/\$asmId.\$db.psl.gz $dbTwoBit \\
         \$db.rna.fa ncbiRefSeqGenomicDiff || true
 
   rm -f $gbdbDir/ncbiRefSeqGenomicDiff.bb
   if [ -s ncbiRefSeqGenomicDiff.bed ]; then
     bedToBigBed -type=bed9+ -tab -as=\${HOME}/kent/src/hg/lib/txAliDiff.as \\
       ncbiRefSeqGenomicDiff.bed process/\$db.chrom.sizes ncbiRefSeqGenomicDiff.bb
     ln -s `pwd`/ncbiRefSeqGenomicDiff.bb $gbdbDir/ncbiRefSeqGenomicDiff.bb
   else
     rm -f ncbiRefSeqGenomicDiff.bed
   fi
 fi
 
 if [ -d "/usr/local/apache/htdocs-hgdownload/goldenPath/archive" ]; then