[ensembl-dev] Fwd: Variant Effect Predictor script

Andy Yates ayates at ebi.ac.uk
Wed May 23 15:07:27 BST 2012


Hi Weihong,

Ensembl Genomes have not released version 14 which is based on the Ensembl 67 APIs. Until they do so, which is scheduled for May 29th, you will have to use the VEP compatible with the version 66 API or specify a -db_version 66 flag on your command line & hope 66 & 67 are compatible enough for this to work.

All the best,

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 23 May 2012, at 13:37, Weihong Qi wrote:

> 
> 
> -------- 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 pagehttp://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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