[ensembl-dev] Variant Effect Predictor error

[Radhika Bartaula]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150203/474d23a8/attachment.html>