[ensembl-dev] VEP unable to connect to Ensembl Genomes
Nikolas Pontikos
n.pontikos at ucl.ac.uk
Tue Jul 28 16:21:28 BST 2015
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
>> >>>>
>> >>>>
>> >>>> _______________________________________________
>> >>>> Dev mailing list Dev at ensembl.org
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>> >>>>
>> >>>>
>> >>>>
>> >>>> _______________________________________________
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>> >>
>> >>
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