[ensembl-dev] request for adding Sz pombe to VEP downloading list

Yutze Li liyutze.seikiri at gmail.com
Thu Sep 20 11:41:07 BST 2018


Adding --offline option fixed the problem. But still wish you can add
fission yeast to the list.
Best.
2018年9月20日(木) 18:34 Yutze Li <liyutze.seikiri at gmail.com>:

> I found the pre-built genome cache of fission yeast schizosaccharomyces
> pombe was on the ftp but not on the list when running the INSTALL.pl of VEP.
> Also, adding the cache downloaded and uncompressed from the ftp to
> my ~/.vep/ did not work.
> My command and the error message goes like:
>
> $ vep --cache --species schizosaccharomyces_pombe --cache_version 40 \
>
> >     --appris --biotype --pick --symbol --tsl --distance 100 \
>
> >     -i $BASE.filter.vcf -o $BASE.ann.vcf
>
>
> -------------------- WARNING ----------------------
>
> MSG: schizosaccharomyces_pombe 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)    = Thu Sep 20 18:16:26 2018
>
> Ensembl API version = 93
>
> ---------------------------------------------------
>
>
> -------------------- EXCEPTION --------------------
>
> MSG: Can not find internal name for species 'schizosaccharomyces_pombe'
>
> STACK Bio::EnsEMBL::Registry::get_adaptor
> /Users/lytzeseikiri/biotools/ensembl-vep/Bio/EnsEMBL/Registry.pm:1111
>
> STACK Bio::EnsEMBL::VEP::BaseVEP::get_adaptor
> /Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:308
>
> STACK Bio::EnsEMBL::VEP::BaseVEP::get_database_assembly
> /Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:419
>
> STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection
> /Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:123
>
> STACK Bio::EnsEMBL::VEP::Runner::init
> /Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:118
>
> STACK Bio::EnsEMBL::VEP::Runner::run
> /Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
>
> STACK toplevel /Users/lytzeseikiri/biotools/ensembl-vep/vep:224
>
> Date (localtime)    = Thu Sep 20 18:16:26 2018
>
> Ensembl API version = 93
>
> ---------------------------------------------------
>
>
> Thanks.
>
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