[ensembl-dev] Uncached variants + Offline mode

[Sebastian Ginzel]

Hi Will,

the --write-cache option was enabled, I don't remember why or who 
enabled it. I think I can safely remove it from my command line, but I 
guess I should re-download the cache?

Regards,
Sebastian Ginzel

On 01.10.2015 17:07, Will McLaren wrote:
> 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 
> <mailto: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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