[ensembl-dev] silent VEP failures

Will McLaren wm2 at ebi.ac.uk
Mon Oct 13 11:49:58 BST 2014

Hi Allison,

I'll take a look at this.

The undef condition is required as some genomic regions will be empty, but
the VEP could handle this way better by checking the file exists first.

Thanks for spotting it


On 10 October 2014 20:15, Allison Regier <aregier at genome.wustl.edu> wrote:

> I’ve been investigating some inconsistent behavior with VEP, and finally
> traced it to an out of memory error that was simply being swallowed up.  In
> load_dumped_transcript_cache in VEP.pm, we sometimes run out of memory,
> which causes the `open` to fail.  We do see the warning message "Could not
> find cache for …”, but since our pipelines are largely automated, warning
> messages don’t mean very much to us.  The variants in these regions end up
> falsely annotated as Intergenic, when many of them should have a transcript
> annotation.  It would be nice to expose this type of error condition more
> obviously.
> For example, the line:
> open my $fh, $config->{compress}." ".$dump_file." |" or return undef;
> could be changed to
> open my $fh, $config->{compress}." ".$dump_file." |" or die “ERROR $!";
> I can’t think of a time when we would want to ignore a failure to open a
> file handle.
> thanks!
> Allison Regier
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