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

mag mr6 at ebi.ac.uk
Mon Jul 20 12:03:49 BST 2015


Hi Mollie,

For the GRCh37 archive, there is currently no limit for the VEP cache, 
as it is not too space consuming.
We can hence guarantee that we can host at least one year worth of releases.

Should we start running out of space and need to set limits, we will try 
to make an informed decision based on users' needs, so please do let us 
know about your use case.

It is also worth noting that, as the GRCh37 assembly is not changing any 
more, the fasta file is the same and will remain that way.
As for the caches, as the data is not updated every release, it is 
possible to re-use the same cache for several releases, meaning more 
releases are kept for the same space.
We will attempt to support milestones, like the 1000 genomes phase 3 
data, as long as possible.

For GRCh38 and the live site, ftp archives currently go back 60 
releases, which is longer than VEP has been available.


Regards,
Magali

On 17/07/2015 15:04, Ullman-Cullere, Mollie wrote:
> Question - if we want to remain stable on an older release of VEP and need to do a fresh install for running in offline mode, how long are the previous versions of VEP with associated cache and fasta files available?
>
> Thanks in advance,
> Mollie
>
> -----Original Message-----
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of mag
> Sent: Friday, July 17, 2015 6:33 AM
> To: dev at ensembl.org
> Subject: Re: [ensembl-dev] VEP unable to connect to Ensembl Genomes
>
> 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
>>>>
>>>>
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