[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
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