[ensembl-dev] VEP regulatory cache

Will McLaren wm2 at ebi.ac.uk
Wed Dec 5 09:52:02 GMT 2012


Hi Chris,

I think that's a bug that's been patched on the 66 CVS branch; the version
of the library you are using has not been patched. I don't know who
monitors/updates these, but a CVS update should fix it.

Is there any reason why you're not using the latest version of VEP (2.7,
Ensembl API 69)?

Regards

Will McLaren
Ensembl Variation


On 5 December 2012 09:12, <cj5 at sanger.ac.uk> wrote:

> Hi
>
> I am running the VEP, version 2.4 with the following options:
> --regulatory
> --offline
> --sift b
> --polyphen b
> --condel b
> --gene
> --hgnc
> --format vcf
> --force_overwrite
> --cache
> --dir <dir to human cache>
>
> and the script crashes with:
>
> Can't call method "length" on unblessed reference
> at
> /software/vertres/lib/all/ensembl/66/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1919, <STDIN> line 2154.
>
> Removing the --offline option solves it, I guess the regulatory cache is
> incomplete?
>
> Thanks
> Chris
>
>
>
>
>
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