a1d34750a532bea424b58b6c27f9732b3c95ea73
hiram
  Thu Sep 30 12:06:55 2021 -0700
fix broken command syntax no redmine

diff --git src/hg/utils/automation/asmHubAssembly.pl src/hg/utils/automation/asmHubAssembly.pl
index 0b3c011..7134730 100755
--- src/hg/utils/automation/asmHubAssembly.pl
+++ src/hg/utils/automation/asmHubAssembly.pl
@@ -80,33 +80,33 @@
 blocks.  The relative order and orientation of the contigs
 within a scaffold is always known; therefore, a line is drawn in the graphical
 display to bridge the blocks.</p>
 <p>
 This assembly has $partCount component parts, with the following principal types of parts:
 <ul>
 _EOF_
     ;
 open (GL, "zcat $agpFile | grep -v '^#' | awk -F'\t' '\$5 != \"N\" && \$5 != \"U\"' | awk '{print \$5}' | sort | uniq -c | sort -n|") or die "can not read $asmId.agp.gz";
 while (my $line = <GL>) {
    chomp $line;
    $line =~ s/^\s+//;
    my ($count, $type) = split('\s+', $line);
    my $singleMessage = "";
    if ((1 == $count) && (("F" eq $type) || ("O" eq $type))) {
-       my $chr = `zcat $agpFile | grep -v '^#' | awk -F'\t' '\$5 == \"$type\" | cut -f1'`;
+       my $chr = `zcat $agpFile | grep -v '^#' | awk -F'\t' '\$5 == \"$type\"' | cut -f1`;
        chomp $chr;
-       my $frag = `zcat $agpFile | grep -v '^#' | awk -F'\t' '\$5 == \"$type\" | cut -f6'`;
+       my $frag = `zcat $agpFile | grep -v '^#' | awk -F'\t' '\$5 == \"$type\"' | cut -f6`;
        chomp $frag;
        $singleMessage = sprintf("(%s/%s)", $chr, $frag);
    }
    if (exists ($goldTypes{$type}) ) {
       if (length($singleMessage)) {
          printf "<li>%s - one %s %s</li>\n", $type, $goldTypes{$type}, $singleMessage;
       } else {
          printf "<li>%s - %s (count: %s)</li>\n", $type, $goldTypes{$type}, &AsmHub::commify($count);
       }
    } else {
       printf STDERR "'%s'\n", $line;
       die "asmHubAssembly.pl: missing AGP contig type definition: $type";
    }
 }
 close (GL);