47df01a42e26269a5c952013a35cb5633e3c0f45
angie
  Tue Jun 3 11:10:06 2025 -0700
Check for existence of bedGraph file before running bedGraphToBigWig.

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index 1afd407ae34..152ee32d2e0 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -75,31 +75,33 @@
     nextstrainInformative.bb
 
 # bigWig for the tree parsimony scores track for David
 bedGraphToBigWig nextstrainParsimony.bedGraph $chromSizes nextstrainParsimony.bw
 
 # Max's nextstrainSamples*.bedGraph allele count bigWigs:
 for i in nextstrainSamples*.vcf.gz; do
     base=`basename $i .vcf.gz`
     zcat $i \
     | grep -v '#' \
     | perl -wne '@w=split("\t");
                  $w[7] =~ m/AC=(\d+)[\d,]*;AN=(\d+)/ ||
                           die "Cant find AC and AN in |$w[7]|";
                  print join("\t", $w[0], $w[1]-1, $w[1], (sprintf "%.06f", $1 / $2)) . "\n";' \
       > $base.bedGraph
+    if [ -s $base.bedGraph ]; then
         bedGraphToBigWig $base.bedGraph $chromSizes $base.bigWig
+    fi
 done
 
 # Install public track files
 mkdir $ottoDir/install
 cp -pf $runDir/nextstrainGene.bb $runDir/nextstrain*Clade.bb \
     $runDir/nextstrain*.vcf.gz{,.tbi} \
     $runDir/nextstrain*.nh \
     $runDir/nextstrainSamples*.bigWig \
     $ottoDir/install/
 rm -rf $ottoDir/current.bak
 mv -f $ottoDir/current $ottoDir/current.bak
 mv $ottoDir/install $ottoDir/current
 rm -r $gbdbDir
 mkdir $gbdbDir
 ln -sf $ottoDir/current/nextstrainGene.bb $ottoDir/current/nextstrain*Clade.bb \