<p dir="ltr">Sorry Guillermo, I'm running out of ideas. </p>
<p dir="ltr">Does the test unit run OK?</p>
<p dir="ltr">perl ensembl-tools/scripts/variant_effect_predictor/t/variant_effect_predictor.t</p>
<p dir="ltr">Will</p>
<div class="gmail_quote">On 4 Jun 2015 12:27, "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 Will,<br>
<br>
I'm getting the exact same error with example_GRCh37.vcf:<br>
<pre>ERROR: Could not detect input file format
</pre>
<br>
I've made a test script as you suggest with the following code and I
don't get any error:<br>
<br>
<pre>#!/usr/bin/env perl
use strict;
use Bio::EnsEMBL::Variation::Utils::VEP qw(detect_format);</pre>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div>On 04/06/15 13:12, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<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" target="_blank">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>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and
subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info:
<a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<br>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<br>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
</div>
<br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div>