[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
>>
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>
>
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