[ensembl-dev] GRCh37 - homo_sapiens is not a valid species name (check DB and API version)
Laurent Gil
lgil at ebi.ac.uk
Tue Oct 30 10:05:09 GMT 2018
Dear Rares,
Then this might be something to do with some elements of the Ensembl API
being in a different version (i.e. not "release/94"): do you have
ensembl-vep and the other ensembl APIs in version 94 ?
To check the installer VEP version:
cd <path_to_ensembl-vep>/ensembl-vep
git branch | grep \* | cut -d ' ' -f2
And the following command will list the versions of the other Ensembl
APIs installed for VEP (ensembl, ensembl-variation,
ensembl-funcgen,ensembl-io):
grep release <path_to_ensembl-vep>/ensembl-vep/.version/*
For instance you should see:
.version/ensembl:release 94
.version/ensembl-funcgen:release 94
.version/ensembl-io:release 94
.version/ensembl-variation:release 94
Best regards,
Laurent
On 29/10/2018 16:40, Rares Vernica wrote:
> Hi Laurent,
>
> --refseq is intentional and I do have the Refseq cache.
>
> Thanks,
> Rares
>
> On Mon, Oct 29, 2018 at 2:26 AM Laurent Gil <lgil at ebi.ac.uk
> <mailto:lgil at ebi.ac.uk>> wrote:
>
> Dear Rares,
>
> Looking at you command line, it seems that you only have the cache
> for the Ensembl transcripts but you are using the flag "--refseq"
> in combination with the flag "--cache", which means that VEP is
> looking for the Refseq transcript cache repository:
> ~/.vep/homo_sapiens_*refseq*/94_GRCh37/.
> If you don't have it, you will need to install it:
> ftp://ftp.ensembl.org/pub/release-94/variation/VEP/homo_sapiens_refseq_vep_94_GRCh37.tar.gz
>
> You can do it via the VEP installer or you can install it manually
> in few steps:
>
> cd ~/.vep
> curl -O ftp://ftp.ensembl.org/pub/release-94/variation/VEP/homo_sapiens_refseq_vep_94_GRCh37.tar.gz
> tar xzfhomo_sapiens_refseq_vep_94_GRCh37.tar.gz
>
>
> Best regards,
>
> Laurent
>
> On 29/10/2018 04:07, Rares Vernica wrote:
>> Hello,
>>
>> I'm having trouble with the public database when using the GRCh37
>> assembly. This is what I run:
>>
>> > ./vep --cache --refseq --assembly GRCh37 --fasta
>> ~/.vep/homo_sapiens/94_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz
>> --input_file 1.tsv --port 3337
>>
>> -------------------- WARNING ----------------------
>> MSG: homo_sapiens is not a valid species name (check DB and API
>> version)
>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1334
>> CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 1109
>> Date (localtime) = Mon Oct 29 03:49:22 2018
>> Ensembl API version = 94
>> ---------------------------------------------------
>>
>> -------------------- EXCEPTION --------------------
>> MSG: Can not find internal name for species 'homo_sapiens'
>> STACK Bio::EnsEMBL::Registry::get_adaptor
>> /usr/local/src/ensembl-vep/Bio/EnsEMBL/Registry.pm:1111
>> STACK Bio::EnsEMBL::VEP::BaseVEP::get_adaptor
>> /usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:307
>> STACK Bio::EnsEMBL::VEP::BaseVEP::get_database_assembly
>> /usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:419
>> STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection
>> /usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:123
>> STACK Bio::EnsEMBL::VEP::Runner::init
>> /usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:118
>> STACK Bio::EnsEMBL::VEP::Runner::run
>> /usr/local/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
>> STACK toplevel ./vep:224
>> Date (localtime) = Mon Oct 29 03:49:22 2018
>> Ensembl API version = 94
>> ---------------------------------------------------
>>
>> It works with --online but I would like to use the /Variant
>> identifiers/
>> <https://uswest.ensembl.org/info/docs/tools/vep/vep_formats.html#id>
>> input format and that does not work with --offline.
>>
>> Any ideas what I'm doing wrong?
>>
>> Thanks!
>> Rares
>>
>> _______________________________________________
>> Dev mailing listDev at ensembl.org <mailto: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/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20181030/02ff68a8/attachment.html>
More information about the Dev
mailing list