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Hi again Will,<br>
<br>
I'm trying with latest ensembl 80.<br>
If I don't specify <b>-format vcf</b> I get the following error:<br>
<br>
<pre>perl ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl -i input.vcf -database --force_overwrite
2015-06-04 11:36:59 - Starting...
ERROR: Could not detect input file format</pre>
<br>
If I force format with<b> -format vcf </b>I get all the errors.
(see error log attached). I'm using the same input.vcf file I posted
yesterday.<br>
Just to discard it's not VCF, I've installed a fresh linux on
virtual machine and just cloned and setup Ensembl and Bioperl. On
fresh Linux install I was only asked to install MySQL perl module (I
installed it via CPAN).<br>
It's working like a cake. <br>
<br>
I discard there's a problem with the input VCF because I'm using
exactly the input over the two environments (and the same one you
used to test it yesterday) <br>
<br>
So my question is: Does VEP script use any other library,
environment variable or tool which may be interfering?<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<br>
<div class="moz-cite-prefix">On 04/06/15 09:32, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote cite="mid:556FFF0F.7080106@sistemasgenomicos.com"
type="cite">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
Hi again Will,<br>
<br>
I've completly cleaned PERL5LIB environment var. I've been testing
changing between bioperl 1.2.3 and bioperl 1.6.1 and got same
warnings/errors.<br>
I've cloned again all 79 API like you suggested in a new tmp
location and included it in $PERL5LIB.<br>
<br>
<pre><b>echo $PERL5LIB </b></pre>
/share/apps/local/bioperl-live:/share/gluster/tests/gmarco/tmp/ensembl/modules:/share/gluster/tests/gmarco/tmp/ensembl-funcgen/modules:/share/gluster/tests/gmarco/tmp/ensembl-variation/modules<br>
<br>
<pre><b>ll /share/gluster/tests/gmarco/tmp</b></pre>
total 20<br>
drwxrwxr-x 8 gmarco users 4096 jun 4 08:44 ensembl<br>
drwxrwxr-x 8 gmarco users 146 jun 4 08:46 ensembl-funcgen<br>
drwxrwxr-x 5 gmarco users 64 jun 4 08:43 ensembl-tools<br>
drwxrwxr-x 10 gmarco users 4096 jun 4 08:45 ensembl-variation<br>
<br>
<pre><b>perl ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl -i input.vcf -database --force_overwrite</b></pre>
2015-06-04 09:29:13 - Starting...<br>
ERROR: Could not detect input file format<br>
<br>
If use the following flags <b>-format vcf</b> <b>-vcf </b>then
I start getting all those errors (see yesterday log).<br>
<br>
Is there any other Perl lib or requirement I could be missing? As
I said it's very weird I have 0 problems with Ensembl 75 local
API.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 03/06/15 18:14, Will McLaren
wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX1kijc_+SGUoxRLnZHfKwOYsP0PvvMsnUf00Mih600Tgg@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="https://github.com/Ensembl/ensembl.git">https://github.com/Ensembl/ensembl.git</a></div>
<div>git clone --branch release/79 <a moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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 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"> 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 moz-do-not-send="true"
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
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>
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