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

[Nikolas Pontikos]

Yes I've just witnessed the same problem.
Code used to work, nothing changed and stopped working.
Something might have changed on the server side.
Adding the --offline flag seems to have fixed it.
This is the error message below:


#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

version 78

By Will McLaren (wm2 at ebi.ac.uk)

Configuration options:

assembly           GRCh37
canonical          1
check_alleles      1
check_existing     1
core_type          core
database           1
dir                /home/rmhanpo/.vep
dir_plugins        /home/rmhanpo/.vep/Plugins
fasta
/scratch2/vyp-scratch2/reference_datasets/human_reference_sequence/human_g1k_v37.fasta
force_overwrite    1
format             vcf
host               ensembldb.ensembl.org
input_file         chr22-single.vcf
no_progress        1
output_file        VEP_22.vcfout
polyphen           b
port               3337
sift               b
species            homo_sapiens
stats              HASH(0x2d671c0)
symbol             1
vcf                1
verbose            1

--------------------

Will only load v78 databases
No core-like databases found. Check your DB_VERSION (used '78')
No variation databases found
No funcgen databases found
No Compara databases found
No ancestral database found
No ontology database found
No production database or adaptor found

-------------------- WARNING ----------------------
MSG: homo_sapiens is not a valid species name (check DB and API version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1200
CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 985
Date (localtime)    = Thu Jul 16 22:52:00 2015
Ensembl API version = 78
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: Can not find internal name for species 'homo_sapiens'
STACK Bio::EnsEMBL::Registry::get_adaptor
/cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:987
STACK main::connect_to_dbs
/cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl:1161
STACK main::configure
/cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl:766
STACK toplevel /cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl:140
Date (localtime)    = Thu Jul 16 22:52:00 2015
Ensembl API version = 78
---------------------------------------------------




On 9 June 2015 at 10:40, Nikolai Adamski (JIC)
<Nikolai.Adamski at jic.ac.uk> wrote:
> 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>
> 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
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>