[ensembl-dev] GRCh37 - homo_sapiens is not a valid species name (check DB and API version)

[Rares Vernica]

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> 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 ~/.vepcurl -O ftp://ftp.ensembl.org/pub/release-94/variation/VEP/homo_sapiens_refseq_vep_94_GRCh37.tar.gztar xzf homo_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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