<div dir="ltr">Thanks Matthew for the detective work.<div><br></div><div>I've removed the \R from the split function and replaced it with what perldoc says it is shorthand for; tests pass OK and it seems to work on the Windows input file that prompted me to make this change in the first place.</div><div><br></div><div>I've patched the fix to release/79 and release/80, so Guillermo I'd appreciate if you could update your ensembl-tools checkout and give this a test run for me.</div><div><br></div><div>Thanks everyone</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 4 June 2015 at 19:17, Healy, Matthew <span dir="ltr"><<a href="mailto:Matthew.Healy@bms.com" target="_blank">Matthew.Healy@bms.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="white" lang="EN-US" link="blue" vlink="purple">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">The \R was added in Perl 5.10.0:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a href="http://perldoc.perl.org/5.10.0/perldelta.html" target="_blank">http://perldoc.perl.org/5.10.0/perldelta.html</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in"><b><span style="color:windowtext">Vertical and horizontal whitespace, and linebreak</span></b><span style="color:windowtext">
<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in">
<span style="color:windowtext">Regular expressions now recognize the </span><span style="font-size:10.0pt;font-family:"Courier New";color:windowtext">\v</span><span style="color:windowtext"> and
</span><span style="font-size:10.0pt;font-family:"Courier New";color:windowtext">\h</span><span style="color:windowtext"> escapes that match vertical and horizontal whitespace, respectively.
</span><span style="font-size:10.0pt;font-family:"Courier New";color:windowtext">\V</span><span style="color:windowtext"> and
</span><span style="font-size:10.0pt;font-family:"Courier New";color:windowtext">\H</span><span style="color:windowtext"> logically match their complements.<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:.5in">
<span style="font-size:10.0pt;font-family:"Courier New";color:windowtext">\R</span><span style="color:windowtext"> matches a generic linebreak, that is, vertical whitespace, plus the multi-character sequence
</span><span style="font-size:10.0pt;font-family:"Courier New";color:windowtext">"\x0D\x0A"</span><span style="color:windowtext"> .<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<div>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:.5in"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Guillermo Marco Puche<br>
<b>Sent:</b> 04 June, 2015 2:10 PM<br>
<b>To:</b> <a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a></span></p><div><div class="h5"><br>
<b>Subject:</b> Re: [ensembl-dev] VEP 79 API problems<u></u><u></u></div></div><p></p>
</div>
</div><div><div class="h5">
<p class="MsoNormal" style="margin-left:.5in"><u></u> <u></u></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">Yes I guess it's clear Perl version is the problem. I'll remove \R from this line in the script until I can update Perl version in my work environment.<br>
<br>
As always, thank you for your fantastic support.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
El 04/06/2015 a las 18:19, Healy, Matthew escribió:<u></u><u></u></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">In the regex documentation for Perl 5.8.8 there is no mention of \R (there is of course \r lowercase), so the Perl version probably
is the issue:</span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a href="http://perldoc.perl.org/5.8.8/perlre.html" target="_blank">http://perldoc.perl.org/5.8.8/perlre.html</a></span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:1.0in"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [<a href="mailto:dev-bounces@ensembl.org" target="_blank">mailto:dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Will McLaren<br>
<b>Sent:</b> 04 June, 2015 12:12 PM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP 79 API problems</span><u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">I'm wondering if 5.8.8 has different regex handling to newer Perl versions. Someone else in the Ensembl team may know better than me on this one.<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">I believe the Ensembl project now recommends at least 5.10 (according to <a href="http://www.ensembl.org/info/docs/api/api_installation.html" target="_blank">http://www.ensembl.org/info/docs/api/api_installation.html</a> at least);
most people in the wild use 5.14 or 5.16 AFAIK.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">If you can possibly try a newer version of Perl this may solve your issues. Perlbrew is a nice way to manage different versions and module sets <a href="http://perlbrew.pl/" target="_blank">http://perlbrew.pl/</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">Will<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 4 June 2015 at 17:02, Guillermo Marco Puche <<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>> wrote:<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">Hello Will,<br>
<br>
Wrong behavior machine has Centos 5.4 and Perl v5.8.8 built for x86_64-linux-thread-multi.<br>
<br>
So should I completly remove ?<u></u><u></u></p>
<pre style="margin-left:1.0in"><b> foreach my $line(split /\r|\R/) {</b><u></u><u></u></pre>
<p class="MsoNormal" style="margin-left:1.0in"><br>
I was thinking about just removing \R from regex.<br>
<br>
Regards,<br>
Guillermo.<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 04/06/15 17:49, Will McLaren wrote:<u></u><u></u></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal" style="margin-left:1.0in">Thanks <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">I had forgotten about that change. You could just edit the script and change or even remove the regexp:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">foreach my $line(($_)) {<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">What's your Perl version and system architecture? I'm surprised this has not caught anyone else out.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">Will<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 4 June 2015 at 14:47, Guillermo Marco Puche <<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>> wrote:<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
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):<u></u><u></u></p>
<pre style="margin-left:1.0in"><b> # split again to avoid Windows character nonsense</b><u></u><u></u></pre>
<pre style="margin-left:1.0in"><b> foreach my $line(split /\r|\R/) {</b><u></u><u></u></pre>
<p class="MsoNormal" style="margin-left:1.0in"><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. <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 04/06/15 15:16, Will McLaren wrote:<u></u><u></u></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p style="margin-left:1.0in">Sorry Guillermo, I'm running out of ideas. <u></u><u></u></p>
<p style="margin-left:1.0in">Does the test unit run OK?<u></u><u></u></p>
<p style="margin-left:1.0in">perl ensembl-tools/scripts/variant_effect_predictor/t/variant_effect_predictor.t<u></u><u></u></p>
<p style="margin-left:1.0in">Will<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 4 Jun 2015 12:27, "Guillermo Marco Puche" <<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>> wrote:<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">Hi Will,<br>
<br>
I'm getting the exact same error with example_GRCh37.vcf:<u></u><u></u></p>
<pre style="margin-left:1.0in">ERROR: Could not detect input file format<u></u><u></u></pre>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<br>
I've made a test script as you suggest with the following code and I don't get any error:<u></u><u></u></p>
<pre style="margin-left:1.0in">#!/usr/bin/env perl<u></u><u></u></pre>
<pre style="margin-left:1.0in"> <u></u><u></u></pre>
<pre style="margin-left:1.0in">use strict;<u></u><u></u></pre>
<pre style="margin-left:1.0in">use Bio::EnsEMBL::Variation::Utils::VEP qw(detect_format);<u></u><u></u></pre>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<br>
Regards,<br>
Guillermo.<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 04/06/15 13:12, Will McLaren wrote:<u></u><u></u></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p style="margin-left:1.0in">Hi again<u></u><u></u></p>
<p style="margin-left:1.0in">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.<u></u><u></u></p>
<p style="margin-left:1.0in">You could write a short script to test the method, just import detect_format from Bio:EnsEMBL::Variation::Utils::VEP<u></u><u></u></p>
<p style="margin-left:1.0in">Does it detect the example_GRCh37.vcf format correctly?<u></u><u></u></p>
<p style="margin-left:1.0in">The file you shared on Dropbox works fine for me on my Mac and a Linux box.
<u></u><u></u></p>
<p style="margin-left:1.0in">Will<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 4 Jun 2015 10:44, "Guillermo Marco Puche" <<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>> wrote:<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
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:<u></u><u></u></p>
<pre style="margin-left:1.0in">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<u></u><u></u></pre>
<pre style="margin-left:1.0in">2015-06-04 11:36:59 - Starting...<u></u><u></u></pre>
<pre style="margin-left:1.0in">ERROR: Could not detect input file format<u></u><u></u></pre>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<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>
<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 04/06/15 09:32, Guillermo Marco Puche wrote:<u></u><u></u></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
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.<u></u><u></u></p>
<pre style="margin-left:1.0in"><b>echo $PERL5LIB </b><u></u><u></u></pre>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
/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<u></u><u></u></p>
<pre style="margin-left:1.0in"><b>ll /share/gluster/tests/gmarco/tmp</b><u></u><u></u></pre>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
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<u></u><u></u></p>
<pre style="margin-left:1.0in"><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><u></u><u></u></pre>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
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.<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 03/06/15 18:14, Will McLaren wrote:<u></u><u></u></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal" style="margin-left:1.0in">Hi again, <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">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.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">See commands I used and input below.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">Perhaps you haven't got release/79 of ensembl-tools too?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">Have you tried running the installer from within ensembl-tools/scripts/variant_effect_predictor? This shouldn't affect your PERL5LIB or other git checkouts.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">Will<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">===================<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">mkdir ~/src/tmp<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">cd ~/src/tmp<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl-tools.git" target="_blank">
https://github.com/Ensembl/ensembl-tools.git</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl.git" target="_blank">
https://github.com/Ensembl/ensembl.git</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl-variation.git" target="_blank">
https://github.com/Ensembl/ensembl-variation.git</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl-funcgen.git" target="_blank">
https://github.com/Ensembl/ensembl-funcgen.git</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">export PERL5LIB=ensembl/modules:ensembl-variation/modules:ensembl-funcgen/modules:/Users/will/src/bioperl-1.2.3/:/Users/will/src/lib/perl5/<u></u><u></u></p>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">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<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:09:54 - Starting...<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:09:54 - Detected format of input file as vcf<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:09:54 - Read 1 variants into buffer<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:09:54 - Reading transcript data from cache and/or database<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">[================================================================================================================================] [ 100% ]<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:10:00 - Retrieved 7 transcripts (0 mem, 0 cached, 7 DB, 0 duplicates)<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:10:00 - Analyzing chromosome 1<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:10:00 - Analyzing variants<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">[================================================================================================================================] [ 100% ]<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:10:00 - Calculating consequences<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:10:00 - Processed 1 total variants (0 vars/sec, 0 vars/sec total)<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:10:00 - Wrote stats summary to variant_effect_output.txt_summary.html<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">2015-06-03 17:10:00 - Finished!<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 3 June 2015 at 16:51, Guillermo Marco Puche <<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>> wrote:<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">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. <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 03/06/15 17:30, Will McLaren wrote:<u></u><u></u></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal" style="margin-left:1.0in">Hi Guille, <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in"><br>
It looks to me like your input is not being parsed properly.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">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.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">If you still have an issue, can you send a line or two of the input that recreates these issues?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">Thanks<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">Will McLaren<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">Ensembl Variation<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">On 3 June 2015 at 16:16, Guillermo Marco Puche <<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>> wrote:<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">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):<u></u><u></u></p>
<p class="MsoNormal" style="margin-left:1.5in">
<u></u><span style="font-size:10.0pt;font-family:Symbol"><span>·<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u>git clone --branch release/79 <a href="https://github.com/Ensembl/ensembl.git" target="_blank">
<span style="color:#5c3566">https://github.com/Ensembl/ensembl.git</span></a> ensembl_79<u></u><u></u></p>
<p style="margin-left:1.0in">PERL5LIB env variable is correctly pointing to the cloned API:
<u></u><u></u></p>
<p class="MsoNormal" style="margin-left:1.5in">
<u></u><span style="font-size:10.0pt;font-family:Symbol"><span>·<span style="font:7.0pt "Times New Roman"">
</span></span></span><u></u>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<u></u><u></u></p>
<p style="margin-left:1.0in">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.<u></u><u></u></p>
<p style="margin-left:1.0in">I've been reading the docs again and I can't seen any additional PERL library requirement.<u></u><u></u></p>
<p style="margin-left:1.0in">Here's the error log: <a href="http://pastebin.com/VvQrkEQZ" target="_blank">
http://pastebin.com/VvQrkEQZ</a><u></u><u></u></p>
<p style="margin-left:1.0in"><br>
Thank you!<u></u><u></u></p>
<p style="margin-left:1.0in">Best regards,<br>
Guille.<u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<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><u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<u></u><u></u></p>
<pre style="margin-left:1.0in">_______________________________________________<u></u><u></u></pre>
<pre style="margin-left:1.0in">Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><u></u><u></u></pre>
<pre style="margin-left:1.0in">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><u></u><u></u></pre>
<pre style="margin-left:1.0in">Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></pre>
</blockquote>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<u></u><u></u></p>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<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><u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<u></u><u></u></p>
<pre style="margin-left:1.0in">_______________________________________________<u></u><u></u></pre>
<pre style="margin-left:1.0in">Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><u></u><u></u></pre>
<pre style="margin-left:1.0in">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><u></u><u></u></pre>
<pre style="margin-left:1.0in">Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></pre>
</blockquote>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<br>
<br>
<br>
<br>
<u></u><u></u></p>
<pre style="margin-left:1.0in">_______________________________________________<u></u><u></u></pre>
<pre style="margin-left:1.0in">Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><u></u><u></u></pre>
<pre style="margin-left:1.0in">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><u></u><u></u></pre>
<pre style="margin-left:1.0in">Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></pre>
</blockquote>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<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><u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<u></u><u></u></p>
<pre style="margin-left:1.0in">_______________________________________________<u></u><u></u></pre>
<pre style="margin-left:1.0in">Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><u></u><u></u></pre>
<pre style="margin-left:1.0in">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><u></u><u></u></pre>
<pre style="margin-left:1.0in">Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></pre>
</blockquote>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<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><u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<u></u><u></u></p>
<pre style="margin-left:1.0in">_______________________________________________<u></u><u></u></pre>
<pre style="margin-left:1.0in">Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><u></u><u></u></pre>
<pre style="margin-left:1.0in">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><u></u><u></u></pre>
<pre style="margin-left:1.0in">Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></pre>
</blockquote>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<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><u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<u></u><u></u></p>
<pre style="margin-left:1.0in">_______________________________________________<u></u><u></u></pre>
<pre style="margin-left:1.0in">Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><u></u><u></u></pre>
<pre style="margin-left:1.0in">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><u></u><u></u></pre>
<pre style="margin-left:1.0in">Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></pre>
</blockquote>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-right:0in;margin-bottom:12.0pt;margin-left:1.0in">
<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><u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:1.0in"> <u></u><u></u></p>
</div>
<div class="MsoNormal" align="center" style="margin-left:.5in;text-align:center">
<hr size="2" width="100%" align="center">
</div>
<p class="MsoNormal" style="margin-left:.5in"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:gray">This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is
intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or
other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
</span><br>
<br>
<br>
<u></u><u></u></p>
<pre style="margin-left:.5in">_______________________________________________<u></u><u></u></pre>
<pre style="margin-left:.5in">Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><u></u><u></u></pre>
<pre style="margin-left:.5in">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><u></u><u></u></pre>
<pre style="margin-left:.5in">Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></pre>
</blockquote>
<p class="MsoNormal" style="margin-left:.5in"><u></u> <u></u></p>
</div></div></div><div><div class="h5">
<hr>
<font face="Arial" size="2" color="Gray">This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you
are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than
the intended recipient is prohibited. </font>
</div></div></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><br></div>