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

Duarte Molha Duarte.Molha at ogt.co.uk
Thu Aug 2 15:51:57 BST 2012


I just did a few more runs and it is not only the Blosum Plugin , all other plugins seem to be giving the same type of error.

So I am guessing from you answer that, for now at least, we cannot use these plugins in conjunction with the fork argument?

Cheers

Duarte

-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 02 August 2012 14:17
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP bugs - Blosum62 plugin incompatible?

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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