[ensembl-dev] problem using variant_effect_predictor.pl on yeast Mito SNPs

Will McLaren wm2 at ebi.ac.uk
Fri Feb 7 08:58:58 GMT 2014


Hi Janet,

We've traced this to a problem in the Ensembl API; our developers are
looking into this now. We'll let you know when we've fixed the issue.

In the meantime, you should have no problems running with the cache; this
is the preferred way to use the VEP in any case.

Regards

Will McLaren
Ensembl Variation


On 5 February 2014 21:07, Janet Young <jayoung at fhcrc.org> wrote:

> Hi there,
>
> I'm exploring using variant_effect_predictor.pl - it looks really cool -
> thanks for all that work!
>
> I'm using it on some of our yeast SNPs (--species
> saccharomyces_cerevisiae). I was getting an error from the script - I've
> narrowed it down to a pretty simple example, and am thinking it might be a
> bug.  I'm wondering if this reproduces with you?
>
> Short story:  I have some SNPs that fail when I run the script in remote
> mode (--database) but work when I run it locally (--cache). Other SNPs work
> both ways. The problem SNPs all seem to come from the "Mito" chromosome
> (but other Mito SNPs work fine).
>
> Long story:  I've attached two vcf files (myProblemSNP.vcf        and
>  mySuccessfulSNP.vcf).
>
> I can annotate both SNPs fine using my local cache - here are the commands
> I used:
>
> variant_effect_predictor.pl --cache --dir
> /home/jayoung/malik_lab/public_databases/Ensembl/VariantEffectPredictorCache
> --species saccharomyces_cerevisiae --input_file myProblemSNP.vcf -o
> myProblemSNP.vcf.annotLocal
>
> variant_effect_predictor.pl --cache --dir
> /home/jayoung/malik_lab/public_databases/Ensembl/VariantEffectPredictorCache
> --species saccharomyces_cerevisiae --input_file mySuccessfulSNP.vcf -o
> mySuccessfulSNP.vcf.annotLocal
>
> (and in case it's relevant, I got my local cache by downloading
> saccharomyces_cerevisiae_vep_74.tar.gz from your ftp site, unpacking that,
> and moving the resulting saccharomyces_cerevisiae dir to my cache dir,
> which is
> /home/jayoung/malik_lab/public_databases/Ensembl/VariantEffectPredictorCache)
>
> However, when I use the script on remote databases, one of the SNPs fails:
>
> ## this one works
> variant_effect_predictor.pl --database --species saccharomyces_cerevisiae
> --input_file mySuccessfulSNP.vcf -o mySuccessfulSNP.vcf.annotRemote
>
> ## this one fails:
> variant_effect_predictor.pl --database --species saccharomyces_cerevisiae
> --input_file myProblemSNP.vcf -o myProblemSNP.vcf.annotRemote
>
> ## here's the on-screen output
> 2014-02-05 12:54:43 - Starting...
> 2014-02-05 12:54:43 - Detected format of input file as vcf
> 2014-02-05 12:54:43 - Read 1 variants into buffer
> 2014-02-05 12:54:43 - Reading transcript data from cache and/or database
> [>
>        ]    [ 0% ]Can't call method "dbID" on an undefined value at
> /home/jayoung/malik_lab_shared/perl/ensembl/modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm
> line 852, <GEN0> line 1.
>
> ## and the output file has only the header.
>
> This is a bit of a mystery - I'm wondering whether this is a bug that
> reproduces on other systems, or whether there's something wrong with my
> installation of the script, or the Ensembl API, or of Bioperl.  I have
> current version of variant_effect_predictor.pl, and should have current
> the ensembl perl API (v74, downloaded Jan 24).
>
> Disclaimer:  I AM using a more recent version of Bioperl than is
> recommended in the installation instructions, I'm afraid (
> http://uswest.ensembl.org/info/docs/api/api_cvs.html) - I needed that for
> other projects, and have not put any time into figuring out how to have old
> and new Bioperls installed simultaneously, and how to point Ensembl towards
> the older one.    I suspect that's not causing the issue I've got here, but
> it's possible.
>
> I'm very curious to hear whether this reproduces for anyone else.
>
> thanks very much,
>
> Janet Young
>
> -------------------------------------------------------------------
>
> Dr. Janet Young
>
> Malik lab
> http://research.fhcrc.org/malik/en.html
>
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., A2-025,
> P.O. Box 19024, Seattle, WA 98109-1024, USA.
>
> tel: (206) 667 4512
> email: jayoung  ...at...  fhcrc.org
>
> -------------------------------------------------------------------
>
>
>
>
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