[ensembl-dev] Variant Effect Predictor error

[mr6 at ebi.ac.uk]

Hi Radhika,

I believe your database connection is against the main Ensembl server.
To run with wheat, you will need to connect to the plant Ensembl Genomes
server.
This can be specified by using the -genomes flag on the command line.

On the documentation page your are using, this is described in the 'Public
database servers' section


Hope that helps,
Magali

> Hi,
> I am having trouble with variant_effect_predictor.pl. I am using this
> script to predict the effect of the SNP’s of wheat(Triticum aestivum)
> exome capture. I installed the tool as explained in the tutorial.
> http://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html
>
> The test data sets runs perfectly fine with human cache but when I run the
> script with Triticum aestivum cache I get the following error. The cache
> for Triticum aestivum is in directory $HOME/.vep. I downloaded the
> prebuilt cache, other species(Plants,
> triticum_asetivum_vep_25_IWGSC2.tar.gz). Then I moved it to       ~
> /.vep/. I followed instructions from
> http://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html.
>
> Here is the error I was getting.
>
> perl variant_effect_predictor.pl<http://variant_effect_predictor.pl/> -i
> /berber/radhika/seq_for_assaf/mpileup_on_rmdup/Zavitan_var.flt_d6_a4.vcf
> --species triticum_aestivum --cache
>
> -------------------- WARNING ----------------------
> MSG: triticum_aestivum 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 Jan 29 11:42:51 2015
> Ensembl API version = 78
> ---------------------------------------------------
> -------------------- EXCEPTION --------------------
> MSG: Can not find internal name for species 'triticum_aestivum'
> STACK Bio::EnsEMBL::Registry::get_adaptor
> /home/radhika/ensembl-tools-release-78/scripts/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:987
> STACK main::connect_to_dbs
> variant_effect_predictor.pl:1161<http://variant_effect_predictor.pl:1161/>
> STACK main::configure
> variant_effect_predictor.pl:766<http://variant_effect_predictor.pl:766/>
> STACK toplevel
> variant_effect_predictor.pl:140<http://variant_effect_predictor.pl:140/>
> Date (localtime)    = Thu Jan 29 11:42:51 2015
> Ensembl API version = 78
>
> I highly appreciate help.
>
> Thank you!
> Radhika
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