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Hi Will,<br>
<br>
I've been comparing variant_effect_predictor script from version 75
vs 79.<br>
After adding a few prints to VEP.pm inside I've spotted the bug.
However I cannot resolve it.<br>
<br>
Those lanes are new from 75 to 79 in VEP script (175 and 176):<br>
<b><br>
</b>
<pre><b> # split again to avoid Windows character nonsense</b></pre>
<pre><b> foreach my $line(split /\r|\R/) {</b></pre>
<br>
<br>
I've checked that script is spliting line each time it finds a
capital R in VCF file as identifying it as a newline character from
Windows. I can't reproduce it in virtual machine since its a fresh
Linux install. In my work environment I'm getting this kind of bug,
so I guess it has something to do with file enconding or locale? Has
anyone else experienced this?<br>
<br>
Now I know where's the error but I've no idea how to solve it.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 04/06/15 15:16, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX36NWJxCsJdomBytg8td+R0JfpS86eGa=PfxDMGDpOQtA@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true" 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 moz-do-not-send="true" 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
moz-do-not-send="true"
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
moz-do-not-send="true"
href="https://github.com/Ensembl/ensembl.git"
target="_blank">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"
target="_blank">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"
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
moz-do-not-send="true"
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 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><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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