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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 class="moz-txt-link-freetext" href="https://www.dropbox.com/sh/felwyoo5kl2mgty/AAC177Digqy-_mEmyk9WvmYba/input.vcf?dl=0">https://www.dropbox.com/sh/felwyoo5kl2mgty/AAC177Digqy-_mEmyk9WvmYba/input.vcf?dl=0</a><br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guille.<br>
<br>
<div class="moz-cite-prefix">On 03/06/15 17:30, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX1emaPyHxf1frOF5ZoQmqn0p-bBDJWC4LLADf7AJ6RbDg@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
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>
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<br>
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