[ensembl-dev] Is it a bug in ensembl_v79?

[Emily Perry]

Please do not send in duplicate emails to both Ensembl helpdesk and 
Ensembl dev as it means that multiple people are working on your query, 
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On 18/03/2015 07:32, namchul ghim wrote:
> After installing Ensembl_v79, I annotated vep cache with GRch37.
> When doing so I got a following message:
> Can't call method "impact" on an undefined value at 
> /mnt/lustre/Tools/VEP/src/ensembl-tools-release-79/scripts/variant_effect_predictor 
>
> /Bio/EnsEMBL/Variation/Utils/VEP.pm line 2379.
>
> When I checked the following source file, there is no definition of 
> imapct() function. There is only function name in the same line.
> Isn't that a bug?
>
> Also, in same condition, annotating only vep cache with GRCh38 version 
> was successful.
>
> What is going on?
>
> Additionally, when I was annotating vep cache with GRCh38 version, 
> there is a warning message in cache file.
> The warning message is as follow:
> WARNING: Could not find variation cache for 22:51000001-52000000
> WARNING: Could not find variation cache for 22:51000001-52000000
> WARNING: Could not find variation cache for 22:51000001-52000000
> WARNING: Could not find variation cache for 22:51000001-52000000
> WARNING: Could not find cache for 22:51000001-52000000
> WARNING: Could not find cache for 22:51000001-52000000
>
> When I checked the actual cache folder, there is no file in such 
> range. Is this something I should consider or can I ignore this message?
>
> For your information, the vep cahce is downloaded in this location:
> ftp://ftp.ensembl.org/pub/release-79/variation/VEP/homo_sapiens_vep_79_GRCh38.tar.gz
>
> Thank you very much!
>
>
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-- 
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

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