[ensembl-dev] silent VEP failures

Will McLaren wm2 at ebi.ac.uk
Mon Oct 13 11:54:46 BST 2014


Probably should have looked at the code first! This is now fixed on GitHub
(master and release/77) with your suggestion (it was already doing a file
exists check first).

Will McLaren
Ensembl Variation

On 13 October 2014 11:49, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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
>
> Will
>
> 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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