f1b5eb49959cc16f05675a7f5e254bc787b99409
hiram
  Wed May 18 09:08:32 2022 -0700
better recognition of the align file presence no redmine

diff --git src/hg/utils/automation/asmHubRepeatMasker.sh src/hg/utils/automation/asmHubRepeatMasker.sh
index af63364..9164bf1 100755
--- src/hg/utils/automation/asmHubRepeatMasker.sh
+++ src/hg/utils/automation/asmHubRepeatMasker.sh
@@ -16,30 +16,33 @@
 
 export dateStamp=`date "+%FT%T %s"`
 
 export asmId=$1
 export rmOutFile=$2
 export destDir=$3
 
 export chrSizes="../../$asmId.chrom.sizes"
 # assume this file name pattern
 export faAlign=`echo "${rmOutFile}" | sed -e 's/sorted.fa.out/fa.align/; s/.gz//;'`
 export RepeatMaskerPath="/hive/data/staging/data/RepeatMasker210401"
 
 if [ -d "${destDir}" ]; then
   cd "${destDir}"
   
+  if [ ! -s "${faAlign}" ]; then
+     faAlign="${faAlign}.gz"
+  fi
   # align file only exists when RM has been run locally, not for NCBI version
   if [ -s "${faAlign}" ]; then
   $RepeatMaskerPath/util/rmToTrackHub.pl -out "${rmOutFile}" -align "${faAlign}"
     # in place same file sort using the -o output option
     sort -k1,1 -k2,2n -o "${asmId}.fa.align.tsv" "${asmId}.fa.align.tsv" &
     sort -k1,1 -k2,2n -o "${asmId}.sorted.fa.join.tsv" "${asmId}.sorted.fa.join.tsv"
     wait
     bedToBigBed -tab -as=$HOME/kent/src/hg/lib/bigRmskAlignBed.as \
       -type=bed3+14 "${asmId}.fa.align.tsv" "${chrSizes}" \
         "${asmId}.rmsk.align.bb" &
     bedToBigBed -tab -as=$HOME/kent/src/hg/lib/bigRmskBed.as -type=bed9+5 \
       "${asmId}.sorted.fa.join.tsv" "${chrSizes}" \
         "${asmId}.rmsk.bb"
     wait
     gzip "${asmId}.fa.align.tsv" &