[ensembl-dev] Uncached variants + Offline mode

[Will McLaren]

Hi Sebastian,

Can you share your full command line?

That line of code should not be triggered unless you have either --database
(which should cause the script to fail on startup) or --write_cache (which
you shouldn't use unless you really know what you're doing!) enabled.

Regards

Will McLaren
Ensembl Variation

On 1 October 2015 at 14:16, Sebastian Ginzel <sginze2s at inf.h-brs.de> wrote:

> Hi,
>
> I am using VEP 80 and use the --offline and --cache option, which usually
> works fine, but now fails on one input file with the message:
>
> Can't call method "db" on an undefined value at
> /path_to_lib/ensembl_80/lib/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 6360, <GEN0> line 190004
>
> After digging into the code I found that this line is called when a
> variant is not available in the cache and VEP tries to retrieve the
> information from the database via through the get_variations_from_region
> function.
>
> The line where the script fails is:
>     if(defined($config->{vfa}->db)) {
>
> Other functions such as 'have_pubmed' have an additional condition which
> prevents the error:
>     if(defined($config->{vfa}) && defined($config->{vfa}->db)) {
>
> I fixed the error for my VEP script by adding the
> "defined($config->{vfa})" condition. But now I am wondering if the error is
> intentional and if not which should be the default return value, if the
> script is running in offline mode.
>
>
> Best wishes,
> Sebastian Ginzel
>
>
>
>
>
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