You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
My bin/HLA-LA.pl looks like this on lines 418-421:
if(system($extraction_command_unmapped) != 0)
{
die "Extraction command $extraction_command_unmapped failed";
}
However I can see there's a change made on 20/07/23 (624f6fd) where the code changes to:
if(system($extraction_command_unmapped) != 0)
{
#die "Extraction command $extraction_command_unmapped failed";
my $count_unmapped = qq($samtools_bin view -\@ $threads_minus_1 $view_T_switch $BAM '*' | awk '{if (\$3 == "*") print \$0}' | wc);
open(COUNT, "$count_unmapped |") or die "Cannot open pipe to count unmapped reads";
my $wc_out = <COUNT>;
chomp($wc_out);
close(COUNT);
die "Cannot parse wc output: '$wc_out'" unless($wc_out =~ /^\s*(\d+)\s+(\d+)\s+/);
my $n_unmapped_reads = $1;
if($n_unmapped_reads != 0)
{
die "Extraction command $extraction_command_unmapped failed - there are unmapped reads [$n_unmapped_reads]";
}
else
{
print "No unmapped reads, you can ignore the samtools warning if one was emitted...\n";
my $extraction_command_unmapped_generateEmptyBAM = qq($samtools_bin view -bo $target_extraction_unmapped -\@ $threads_minus_1 $view_T_switch $BAM '*');
system($extraction_command_unmapped_generateEmptyBAM) and die "Command $extraction_command_unmapped_generateEmptyBAM failed (empty BAM generation, no unmapped reads";
}
}
I was wondering if this difference may be the cause of the error? I tried to alter the code but then I get an error regarding PRG_MHC_GRCh38_withIMGT (HLA-LA is unable to find it although I didn't change the location). Reverting the changes gives back the original error regarding the header.
Hi,
I'm running some samples through HLA*LA and I've been hit by this error.
I found an old issue that dealt with this [https://github.com//issues/63] Is this the current advice? Many thanks.
The text was updated successfully, but these errors were encountered: