[ensembl-dev] VEP unable to connect to Ensembl Genomes
Nikolas Pontikos
n.pontikos at ucl.ac.uk
Sat Jul 25 11:45:14 BST 2015
Hello Magali,
There is no particular reason except that I haven't gotten round to
updating our installation.
Incidentally, what is the most straightforward way of doing an update?
Thanks,
Nikolas.
On 17 July 2015 at 11:33, mag <mr6 at ebi.ac.uk> wrote:
> Hi Nikolas,
>
> Apologies for the misleading information, we officially support 2 releases
> at one given time, the current one and the previous one
> http://grch37.ensembl.org/info/data/mysql.html
>
> The release 79 databases have not yet been cleared up following release 81,
> but we cannot guarantee they will remain available much longer, as this
> depends on the space available on the server.
>
> May I ask if there is a particular reason you are using version 78 and not a
> more recent one?
>
>
> Regards,
> Magali
>
>
> On 17/07/2015 10:56, mag wrote:
>>
>> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> 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/
>>>>
>>> _______________________________________________
>>> 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/
>
>
>
> _______________________________________________
> 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/
More information about the Dev
mailing list