[ensembl-dev] VEP unable to connect to Ensembl Genomes

[Will McLaren]

Hi Nikolai,

The release 80 databases are not yet available.

You may either use --offline to avoid checking the database connection, or
"--db_version 79" to force VEP to connect to the release 79 databases.

Regards

Will McLaren
Ensembl Variation

On 9 June 2015 at 10:24, Nikolai Adamski (JIC) <Nikolai.Adamski at jic.ac.uk>
wrote:

>  Hi,
>
>
>
> I used VEP on wheat data on Friday (5th of June) without problems
> (ensembl-tools-80)
>
>
>
> perl variant_effect_predictor.pl -i input.vcf -o output.txt --cache
> --species triticum_aestivum --cache_version 26
>
>
>
> I tried running more data today, but keep getting error message:
>
>
>
> -------------------- WARNING ----------------------
>
> MSG: triticum_aestivum is not a valid species name (check DB and API
> version)
>
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1198
>
> CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 983
>
> Date (localtime)    = Tue Jun  9 10:20:21 2015
>
> Ensembl API version = 80
>
> ---------------------------------------------------
>
>
>
> -------------------- EXCEPTION --------------------
>
> MSG: Can not find internal name for species 'triticum_aestivum'
>
> STACK Bio::EnsEMBL::Registry::get_adaptor
> /usr/users/celldev/adamskin/Downloads/ensembl-tools-release-80/scripts/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:985
>
> STACK main::connect_to_dbs variant_effect_predictor.pl:1205
>
> STACK main::configure variant_effect_predictor.pl:794
>
> STACK toplevel variant_effect_predictor.pl:142
>
> Date (localtime)    = Tue Jun  9 10:20:21 2015
>
> Ensembl API version = 80
>
> ---------------------------------------------------
>
>
>
> Using the --genomes flag results in the same error message.
>
> Is the server down?
>
>
>
> Many thanks for your help
>
> cheers
>
> nikolai
>
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