[ensembl-dev] VEP unable to connect to Ensembl Genomes
Will McLaren
wm2 at ebi.ac.uk
Thu Jul 30 10:39:51 BST 2015
Hi Nikolas,
Seems like a network issue; you can just download the latest version of VEP
manually and run the installer to get the API.
http://www.ensembl.org/info/docs/tools/vep/script/index.html
Regards
Will
On 28 July 2015 at 16:21, Nikolas Pontikos <n.pontikos at ucl.ac.uk> wrote:
> Thanks Will, however I get an error when I run the update:
>
> cd ensembl/src/ensembl-tools/scripts/variant_effect_predictor
>
> perl INSTALL.pl --UPDATE
>
> Hello! This installer is configured to install v78 of the Ensembl API for
> use by the VEP.
> It will not affect any existing installations of the Ensembl API that you
> may have.
>
> It will also download and install cache files from Ensembl's FTP server.
>
> Checking for newer version of the VEP
> malformed JSON string, neither array, object, number, string or atom, at
> character offset 0 (before "<!DOCTYPE html>\n<!-...") at INSTALL.pl line
> 121.
> [rmhanpo at pchuckle:/cluster/project8/vyp/AdamLevine/software/ensembl/src/ensembl-tools/scripts/variant_effect_predictor$]
> vim INSTALL.pl +121
>
>
>
>
>
>
> On 27 July 2015 at 13:27, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
>> Hi Nikolas,
>>
>> The VEP INSTALL.pl script offers an update option, simply run:
>>
>> perl INSTALL.pl --UPDATE
>>
>> Regards
>>
>> Will McLaren
>> Ensembl Variation
>>
>> On 25 July 2015 at 11:45, Nikolas Pontikos <n.pontikos at ucl.ac.uk> wrote:
>>
>>> 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
>>> >>>>
>>> >>>>
>>> >>>> _______________________________________________
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