[ensembl-dev] silent VEP failures

[Allison Regier]

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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