<div dir="ltr">Hi Janet,<div><br></div><div>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.</div><div><br></div><div>In the meantime, you should have no problems running with the cache; this is the preferred way to use the VEP in any case.</div>
<div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 5 February 2014 21:07, Janet Young <span dir="ltr"><<a href="mailto:jayoung@fhcrc.org" target="_blank">jayoung@fhcrc.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi there,<br>
<br>
I'm exploring using <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> - it looks really cool - thanks for all that work!<br>
<br>
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?<br>
<br>
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).<br>
<br>
Long story: I've attached two vcf files (myProblemSNP.vcf and mySuccessfulSNP.vcf).<br>
<br>
I can annotate both SNPs fine using my local cache - here are the commands I used:<br>
<br>
<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --cache --dir /home/jayoung/malik_lab/public_databases/Ensembl/VariantEffectPredictorCache --species saccharomyces_cerevisiae --input_file myProblemSNP.vcf -o myProblemSNP.vcf.annotLocal<br>
<br>
<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --cache --dir /home/jayoung/malik_lab/public_databases/Ensembl/VariantEffectPredictorCache --species saccharomyces_cerevisiae --input_file mySuccessfulSNP.vcf -o mySuccessfulSNP.vcf.annotLocal<br>
<br>
(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)<br>
<br>
However, when I use the script on remote databases, one of the SNPs fails:<br>
<br>
## this one works<br>
<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --database --species saccharomyces_cerevisiae --input_file mySuccessfulSNP.vcf -o mySuccessfulSNP.vcf.annotRemote<br>
<br>
## this one fails:<br>
<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --database --species saccharomyces_cerevisiae --input_file myProblemSNP.vcf -o myProblemSNP.vcf.annotRemote<br>
<br>
## here's the on-screen output<br>
2014-02-05 12:54:43 - Starting...<br>
2014-02-05 12:54:43 - Detected format of input file as vcf<br>
2014-02-05 12:54:43 - Read 1 variants into buffer<br>
2014-02-05 12:54:43 - Reading transcript data from cache and/or database<br>
[> ] [ 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.<br>
<br>
## and the output file has only the header.<br>
<br>
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 <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>, and should have current the ensembl perl API (v74, downloaded Jan 24).<br>
<br>
Disclaimer: I AM using a more recent version of Bioperl than is recommended in the installation instructions, I'm afraid (<a href="http://uswest.ensembl.org/info/docs/api/api_cvs.html" target="_blank">http://uswest.ensembl.org/info/docs/api/api_cvs.html</a>) - 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.<br>
<br>
I'm very curious to hear whether this reproduces for anyone else.<br>
<br>
thanks very much,<br>
<br>
Janet Young<br>
<br>
-------------------------------------------------------------------<br>
<br>
Dr. Janet Young<br>
<br>
Malik lab<br>
<a href="http://research.fhcrc.org/malik/en.html" target="_blank">http://research.fhcrc.org/malik/en.html</a><br>
<br>
Fred Hutchinson Cancer Research Center<br>
1100 Fairview Avenue N., A2-025,<br>
P.O. Box 19024, Seattle, WA 98109-1024, USA.<br>
<br>
tel: <a href="tel:%28206%29%20667%204512" value="+12066674512">(206) 667 4512</a><br>
email: jayoung ...at... <a href="http://fhcrc.org" target="_blank">fhcrc.org</a><br>
<br>
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<br></blockquote></div><br></div>