[ensembl-dev] silent VEP failures

Allison Regier aregier at genome.wustl.edu
Fri Oct 10 20:15:18 BST 2014

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.


Allison Regier

This email message is a private communication. The information transmitted, including attachments, is intended only for the person or entity to which it is addressed and may contain confidential, privileged, and/or proprietary material. Any review, duplication, retransmission, distribution, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is unauthorized by the sender and is prohibited. If you have received this message in error, please contact the sender immediately by return email and delete the original message from all computer systems. Thank you.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20141010/ba25f1f4/attachment.html>

More information about the Dev mailing list