[ensembl-dev] VEP bugs - Blosum62 plugin incompatible?

Will McLaren wm2 at ebi.ac.uk
Thu Aug 2 14:16:44 BST 2012


Hi Duarte,

I'll take a look at this - in the meantime you may have to disable
forking (remove "--fork 10" from you command line) to use the Blosum62
plugin.

Cheers

Will

On 2 August 2012 14:06, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:
> Dear Developers
>
>
>
> I downloaded the latest VEP script and run it using these parameters:
>
> using the command:
>
>
>
> perl variant_effect_predictor.pl -i example.vcf -o example_annot.vcf --vcf
> --sift b --polyphen b --numbers --domains --regulatory --protein
> --check_existing --verbose --buffer_size 500000 --force_overwrite --gmaf
> --fork 10 --plugin Blosum62
>
>
>
> The script dies with the output:
>
>
>
> Can't use string ("0.524") as a HASH ref while "strict refs" in use at
> /NGS_Tools/bin/VEP_26_testing/Bio/EnsEMBL/Variation/Utils/VEP.pm line 4530,
> <CHILD> line 512.
>
>
>
> This seems to be related with the Plug-in Blosum62... when running the
> script without the Blosum plugin it runs fine
>
>
>
> Any ideas in what might be wrong?
>
>
>
> Best regards,
>
>
>
> Duarte Molha
>
>
>
>
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