[ensembl-dev] Fwd: Variant Effect Predictor script

Weihong Qi Weihong.Qi at fgcz.ethz.ch
Wed May 23 13:37:08 BST 2012



-------- Original Message --------
Subject: 	Variant Effect Predictor script
Date: 	Wed, 23 May 2012 14:34:33 +0200
From: 	Qi Weihong <weihong.qi at fgcz.ethz.ch>
To: 	dev at ensembl.org <dev at ensembl.org>



Dear Ensembl development team,

Recently I installed the VEP script version 2.5 using the install perl 
script.  It runs well with human datasets. But I could not run the 
script against arabidopsis. Could you please help me out?

The command line  was "perl variant_effect_predictor.pl -i test.vcf 
--format vcf -o test.vep -genomes -species arabidopsis_thaliana", which 
was followed the suggestions from the help page 
http://www.ensembl.org/info/docs/variation/vep/vep_script.html#help.

The error messages were:

-------------------- WARNING ----------------------
MSG: arabidopsis_thaliana is not a valid species name (check DB and API 
version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1172
CALLED BY: src/variant_effect_predictor/variant_effect_predictor.pl  
LINE: 653
Ensembl API version = 67
---------------------------------------------------

-------------------- WARNING ----------------------
MSG: arabidopsis_thaliana is not a valid species name (check DB and API 
version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1172
CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 957
Ensembl API version = 67
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: Can not find internal name for species 'arabidopsis_thaliana'
STACK Bio::EnsEMBL::Registry::get_adaptor 
/misc/ngseq/src/variant_effect_predictor/Bio/EnsEMBL/Registry.pm:959
STACK main::get_adaptors 
/usr/local/ngseq/src/variant_effect_predictor/variant_effect_predictor.pl:1054
STACK main::configure 
/usr/local/ngseq/src/variant_effect_predictor/variant_effect_predictor.pl:766
STACK toplevel 
/usr/local/ngseq/src/variant_effect_predictor/variant_effect_predictor.pl:66
Ensembl API version = 67

Many thanks,

Weihong





-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120523/65001d20/attachment.html>


More information about the Dev mailing list