<div dir="ltr">Hi again,<div><br></div><div>I can't recreate the problem with that input file I'm afraid, either on my normal setup or scrubbing PERL5LIB and starting from scratch.</div><div><br></div><div>See commands I used and input below.</div><div><br></div><div>Perhaps you haven't got release/79 of ensembl-tools too?</div><div><br></div><div>Have you tried running the installer from within ensembl-tools/scripts/variant_effect_predictor? This shouldn't affect your PERL5LIB or other git checkouts.</div><div><br></div><div>Will</div><div><br></div><div>===================</div><div><br></div><div>mkdir ~/src/tmp</div><div>cd ~/src/tmp</div><div>git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl-tools.git">https://github.com/Ensembl/ensembl-tools.git</a><br></div><div>git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl.git">https://github.com/Ensembl/ensembl.git</a></div><div>git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl-variation.git">https://github.com/Ensembl/ensembl-variation.git</a><br></div><div>git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl-funcgen.git">https://github.com/Ensembl/ensembl-funcgen.git</a><br></div><div>export PERL5LIB=ensembl/modules:ensembl-variation/modules:ensembl-funcgen/modules:/Users/will/src/bioperl-1.2.3/:/Users/will/src/lib/perl5/<br></div><div><div>perl ensembl-tools/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> -i ~/Downloads/input.vcf -database</div><div>2015-06-03 17:09:54 - Starting...</div><div>2015-06-03 17:09:54 - Detected format of input file as vcf</div><div>2015-06-03 17:09:54 - Read 1 variants into buffer</div><div>2015-06-03 17:09:54 - Reading transcript data from cache and/or database</div><div>[================================================================================================================================] [ 100% ]</div><div>2015-06-03 17:10:00 - Retrieved 7 transcripts (0 mem, 0 cached, 7 DB, 0 duplicates)</div><div>2015-06-03 17:10:00 - Analyzing chromosome 1</div><div>2015-06-03 17:10:00 - Analyzing variants</div><div>[================================================================================================================================] [ 100% ]</div><div>2015-06-03 17:10:00 - Calculating consequences</div><div>2015-06-03 17:10:00 - Processed 1 total variants (0 vars/sec, 0 vars/sec total)</div><div>2015-06-03 17:10:00 - Wrote stats summary to variant_effect_output.txt_summary.html</div><div>2015-06-03 17:10:00 - Finished!</div></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 3 June 2015 at 16:51, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF">
Hi Will,<br>
<br>
I've been checking and I can't see any unintended whitespace or
problem with tabulations.<br>
I've no issues with old vep 75 script and API. I've updated the
Bioperl lib in $PERL5LIB variable from 1.2.3 to 1.6.1 (I didn't see
this change before sorry) however I'm still getting all those
errors.<br>
<br>
Here's a link where you can download the VCF I'm using as input:
<a href="https://www.dropbox.com/sh/felwyoo5kl2mgty/AAC177Digqy-_mEmyk9WvmYba/input.vcf?dl=0" target="_blank">https://www.dropbox.com/sh/felwyoo5kl2mgty/AAC177Digqy-_mEmyk9WvmYba/input.vcf?dl=0</a><br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guille.<div><div class="h5"><br>
<br>
<div>On 03/06/15 17:30, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guille,
<div><br>
It looks to me like your input is not being parsed properly.<br>
</div>
<div><br>
</div>
<div>Check the formatting of your input VCF; double check that
it is valid VCF, and that you haven't got any unintended
whitespace on any of the lines.</div>
<div><br>
</div>
<div>If you still have an issue, can you send a line or two of
the input that recreates these issues?</div>
<div><br>
</div>
<div>Thanks</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 3 June 2015 at 16:16, Guillermo
Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Dear devs,<br>
<br>
I'm trying ensembl 79 VEP.<br>
<br>
This is my dummy input VCF: <a href="http://pastebin.com/kFKWH50q#" target="_blank">http://pastebin.com/kFKWH50q#</a><br>
<br>
I've cloned and installed API from github as always (this
step is repeated for variaton, funcgen and compara):<br>
<ul>
<li>git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl.git" style="word-wrap:break-word;text-decoration:underline;color:rgb(92,53,102)" target="_blank">https://github.com/Ensembl/ensembl.git</a>
ensembl_79</li>
</ul>
<p>PERL5LIB env variable is correctly pointing to the
cloned API: <br>
</p>
<ul>
<li>echo $PERL5LIB <br>
/share/apps/local/bioperl-live:/share/apps/src/ensembl_79/modules:/share/apps/src/ensembl_79-compara/modules:/share/apps/src/ensembl_79-variation/modules:/share/apps/src/ensembl_79-functgenomics/modules</li>
</ul>
<p>However I'm getting a lot of errors I really don't
understand. It seems like a bug with API installation
with me. If I change $PERL5LIB variable to point to 75
API (previous version I was using) I can't reproduce the
errors VEP script works for this old 75 version.<br>
</p>
<p>I've been reading the docs again and I can't seen any
additional PERL library requirement.<br>
</p>
<p>Here's the error log: <a href="http://pastebin.com/VvQrkEQZ" target="_blank">http://pastebin.com/VvQrkEQZ</a><br>
</p>
<p><br>
Thank you!<br>
</p>
<p>Best regards,<br>
Guille.<br>
</p>
</div>
<br>
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</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
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