<div dir="ltr">Hi Guille,<div><br class="">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>
<pre style="white-space:pre-wrap;word-wrap:break-word;margin:0px;color:rgb(51,51,51);font-size:13px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;background-color:rgb(255,255,255)"></pre>
<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>
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<br></blockquote></div><br></div>