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

Nikolai Adamski (JIC) Nikolai.Adamski at jic.ac.uk
Tue Jun 9 10:40:45 BST 2015


Hi Will,

thank you for the quick answer!
Still puzzled though why it seems to have worked last week.

cheers
nikolai

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 09 June 2015 10:35
To: Ensembl developers list
Subject: Re: [ensembl-dev] VEP unable to connect to Ensembl Genomes

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<mailto: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<http://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<http://variant_effect_predictor.pl:1205>
STACK main::configure variant_effect_predictor.pl:794<http://variant_effect_predictor.pl:794>
STACK toplevel variant_effect_predictor.pl:142<http://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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