[ensembl-dev] VEP unable to connect to Ensembl Genomes
mag
mr6 at ebi.ac.uk
Fri Jul 17 10:56:06 BST 2015
Hi Nikolas,
We are currently maintaining 3 releases worth of databases on the
dedicated GRCh37 MySQL server.
As 81 was released yesterday, 78 has now been removed.
You can still access releases 79, 80 and 81 for the GRCh37 assembly.
Hope this helps,
Magali
On 17/07/2015 10:46, Nikolas Pontikos wrote:
> 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
>>
>>
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>>
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