[ensembl-dev] vep warning when using cache

[Guillermo Marco Puche]

Hi Will,

I got the exact same warnings with 79_GRCh38 cache (indexed previosuly 
with convert_cache)
Then I decided to try with 80_GRCh38 cache and API version 80. I didn't 
index it and I'm getting the same warnings. Tomorrow I'll index 
80_GRCh38 cache and report "info.txt".

Regards,
Guillermo.

El 10/06/2015 a las 17:59, Will McLaren escribió:
> Hi Guillermo,
>
> Did you say you had run convert_cache.pl <http://convert_cache.pl> in 
> an earlier email?
>
> This may be the issue here. Can you send on the content of the file 
> [cache_dir]/homo_sapiens/80_GRCh37/info.txt
>
> It may be you need to re-run the convert_cache script, possibly after 
> downloading the original cache again.
>
> Will
>
> On 10 June 2015 at 15:40, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     Dear devs,
>
>     I'm experiencing the following warnings when using vep local cache
>     with variant_effect_predictor script:
>
>         Argument "-/C" isn't numeric in numeric eq (==) at /share/apps/src/ensembl_80-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 6218.
>
>         Use of uninitialized value in split at /share/apps/src/ensembl_80-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 6223.
>
>
>     If no cache is used warnings disappear.
>
>     Input VCF: example_GRCh38.vcf  (inside
>     https://github.com/Ensembl/ensembl-tools/archive/release/80.zip)
>     Cache downloaded from:
>     ftp://ftp.ensembl.org/pub/release-80/variation/VEP/homo_sapiens_vep_80_GRCh38.tar.gz
>
>     Best regards,
>     Guillermo.
>
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