bdc5df573ffaa879405a4e13f10c205fed01c4d1
hiram
  Fri May 1 12:55:06 2026 -0700
explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811

diff --git src/hg/utils/automation/asmHubAllGaps.pl src/hg/utils/automation/asmHubAllGaps.pl
index f0976c83574..290d096a31f 100755
--- src/hg/utils/automation/asmHubAllGaps.pl
+++ src/hg/utils/automation/asmHubAllGaps.pl
@@ -62,21 +62,21 @@
 Any sequence of N's in the assembly is marked as a gap in this track.
 The standard gap track only shows the gaps as annotated in the AGP file:
 <a href="$hubUrl/$agpFileBase" target=_blank>$asmId.agp.gz</a><br>
 The NCBI document
 <a href="https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/"
 target=_blank>AGP Specification</a> describes the format of the AGP file.
 </p>
 <p>
 Gaps are represented as black boxes in this track.
 There is no information in this track about order or orientation
 of the contigs on either side of the gap.
 </p>
 <p>
 _EOF_
     ;
-my $gapCount = `bigBedInfo $allGapsBbi | egrep "itemCount:|basesCovered:" | xargs echo | sed -e 's/itemCount/gap count/; s/basesCovered/bases covered/;'`;
+my $gapCount = `/cluster/bin/x86_64/bigBedInfo $allGapsBbi | egrep "itemCount:|basesCovered:" | xargs echo | sed -e 's/itemCount/gap count/; s/basesCovered/bases covered/;'`;
 chomp $gapCount;
 printf "Gap count and coverage: %s</li>\n", $gapCount;
 
 printf "</p>\n";