[ensembl-dev] VEP unable to connect to Ensembl Genomes
Will McLaren
wm2 at ebi.ac.uk
Mon Jul 27 13:27:11 BST 2015
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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