[ensembl-dev] Thanks - Re: Fwd: Variant Effect Predictor script

[Weihong Qi]

Dear Andy,

Many thanks for your quick response and the helpful tip. By specifying 
-db_version 66, VEP worked with Arabidopsis.

Have a nice weekend,

Weihong

On 5/23/2012 4:07 PM, Andy Yates wrote:
> 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
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/


-- 
Weihong Qi, PhD
Functional Genomics Center Zurich
Uni/ETH Zurich
Winterthurerstrasse 190 / Y32 H66
CH-8057 Zurich

Phone (Fixed line office):  +41 44 635 3964
Phone (Mobile office): +41 44 635 3997
Fax:  +41 44 635 3922
E-mail: weihong.qi at fgcz.ETHZ.ch
Web:  http://www.fgcz.ch