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

Janet Young jayoung at fhcrc.org
Wed Feb 5 21:07:20 GMT 2014


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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