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

Will McLaren wm2 at ebi.ac.uk
Thu Aug 2 15:24:11 BST 2012


Hello again,

This is fixed on branch 68 - please update your ensembl-variation CVS checkout.

Cheers

Will

On 2 August 2012 14:16, Will McLaren <wm2 at ebi.ac.uk> wrote:
> 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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