<p dir="ltr">Hi again</p>
<p dir="ltr">If the script is not detecting the input format then it is almost certainly an issue with the input file. There's very little code that gets run to detect the format, and it's all internal to the VEP code.</p>
<p dir="ltr">You could write a short script to test the method, just import detect_format from Bio:EnsEMBL::Variation::Utils::VEP</p>
<p dir="ltr">Does it detect the example_GRCh37.vcf format correctly?</p>
<p dir="ltr">The file you shared on Dropbox works fine for me on my Mac and a Linux box. </p>
<p dir="ltr">Will</p>
<div class="gmail_quote">On 4 Jun 2015 10:44, "Guillermo Marco Puche" <<a href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF">
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/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -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>On 04/06/15 09:32, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote type="cite">
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/<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -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>On 03/06/15 18:14, Will McLaren
wrote:<br>
</div>
<blockquote 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 href="https://github.com/Ensembl/ensembl-tools.git" target="_blank">https://github.com/Ensembl/ensembl-tools.git</a><br>
</div>
<div>git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl.git" target="_blank">https://github.com/Ensembl/ensembl.git</a></div>
<div>git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl-variation.git" target="_blank">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" target="_blank">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" target="_blank">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><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>
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