<div dir="ltr">Hello Janet,<div><br></div><div>I can confirm this is just a warning and it won't affect your output - I'll create a fix so the warning doesn't appear in future.</div><div><br></div><div>PS don't worry about your BioPerl install being newer - for the purposes of using the VEP the latest version is fine.</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 6 February 2014 18:53, 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"><div style="word-wrap:break-word">Hi there,<div><br></div><div>I think I've found a very minor issue with <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a>. As far as I can tell, it's not affecting the output in any major way (might cause sorting issues - not sure). I'm still at the early stages of using the script, so it's also possible I've messed something up. </div>
<div><br></div><div>Anyway, I'm currently trying the script on some of our drosophila data. If my vcf file has SNPs from a mix of chromosomes with numeric names (e.g. 4) and character names (e.g. 3RHet), I get a sorting error. If I split the vcf file so that the chr 4 and chr 3RHet SNPs are in separate files, there's no error.</div>
<div><br></div><div><div>The output looks OK, I think, but it still seemed worth letting you know about this (I always get a little paranoid that output will be messed up when I see any error - it'd be nice to get it fixed at some point). Looking at VEP.pm I think I can see why that error comes up.</div>
</div><div><br></div><div>I've attached a small example input file. Here's the error:</div><div><div>Argument "3RHet" isn't numeric in numeric comparison (<=>) at /home/jayoung/malik_lab_shared/perl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1235, <GEN0> line 6.</div>
</div><div><br></div><div>and here's the full command and output:</div><div><br></div><div><div><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 drosophila_melanogaster --input_file testCombined3RHetand4small.vcf -o testCombined3RHetand4small.vcf.annotLocal</div>
<div><br></div><div>2014-02-06 10:39:31 - Read existing cache info</div><div>2014-02-06 10:39:35 - Starting...</div><div>2014-02-06 10:39:35 - Detected format of input file as vcf</div><div>2014-02-06 10:39:35 - Read 6 variants into buffer</div>
<div>Argument "3RHet" isn't numeric in numeric comparison (<=>) at /home/jayoung/malik_lab_shared/perl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1235, <GEN0> line 6.</div>
<div>2014-02-06 10:39:35 - Reading transcript data from cache and/or database</div><div>[================================================================================================] [ 100% ]</div><div>2014-02-06 10:39:35 - Retrieved 253 transcripts (0 mem, 253 cached, 0 DB, 0 duplicates)</div>
<div>2014-02-06 10:39:35 - Analyzing chromosome 3RHet</div><div>2014-02-06 10:39:35 - Analyzing variants</div><div>[================================================================================================] [ 100% ]</div>
<div>2014-02-06 10:39:35 - Calculating consequences</div><div>[================================================================================================] [ 100% ]</div><div>2014-02-06 10:39:35 - Analyzing chromosome 4</div>
<div>2014-02-06 10:39:35 - Analyzing variants</div><div>[================================================================================================] [ 100% ]</div><div>2014-02-06 10:39:35 - Calculating consequences</div>
<div>[================================================================================================] [ 100% ]</div><div>2014-02-06 10:39:35 - Processed 6 total variants (6 vars/sec, 6 vars/sec total)</div><div>2014-02-06 10:39:35 - Wrote stats summary to testCombined3RHetand4small.vcf.annotLocal_summary.html</div>
<div>2014-02-06 10:39:35 - Finished!</div></div><div><br></div><div>I have a current version of <a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> (74), and should have a current version of the ensembl perl API (v74, downloaded Jan 24). (as for another question I sent yesterday, here's a 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 don't think that's causing the issue here, though)<br>
</div><div><br></div><div>thanks again,</div><div><br></div><div>Janet Young</div><div><br></div><div><div>------------------------------------------------------------------- </div><div><br></div><div>Dr. Janet Young </div>
<div><br></div><div>Malik lab</div><div><a href="http://research.fhcrc.org/malik/en.html" target="_blank">http://research.fhcrc.org/malik/en.html</a></div><div><br></div><div>Fred Hutchinson Cancer Research Center</div><div>
1100 Fairview Avenue N., A2-025, </div><div>P.O. Box 19024, Seattle, WA 98109-1024, USA.</div><div><br></div><div>tel: <a href="tel:%28206%29%20667%204512" value="+12066674512" target="_blank">(206) 667 4512</a></div><div>
email: jayoung ...at... <a href="http://fhcrc.org" target="_blank">fhcrc.org</a></div><div><br></div><div>------------------------------------------------------------------- </div></div><div></div></div><br><div style="word-wrap:break-word">
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