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<div class="moz-cite-prefix">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:<br>
</div>
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<div class="WordSection1">
<p class="MsoNormal"><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:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a
moz-do-not-send="true"
href="http://perldoc.perl.org/5.8.8/perlre.html">http://perldoc.perl.org/5.8.8/perlre.html</a><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<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"">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a class="moz-txt-link-abbreviated" href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a class="moz-txt-link-freetext" href="mailto:dev-bounces@ensembl.org">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<o:p></o:p></span></p>
</div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">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.<o:p></o:p></p>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in">I believe the
Ensembl project now recommends at least 5.10 (according
to <a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/api_installation.html">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.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in">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 moz-do-not-send="true"
href="http://perlbrew.pl/">http://perlbrew.pl/</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in">Will<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">On 4 June 2015
at 17:02, Guillermo Marco Puche <<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:<o:p></o:p></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">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 ?<o:p></o:p></p>
<pre style="margin-left:.5in"><b> foreach my $line(split /\r|\R/) {</b><o:p></o:p></pre>
<p class="MsoNormal" style="margin-left:.5in"><br>
I was thinking about just removing \R from regex.<br>
<br>
Regards,<br>
Guillermo.<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><o:p> </o:p></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">On
04/06/15 17:49, Will McLaren wrote:<o:p></o:p></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal" style="margin-left:.5in">Thanks
<o:p></o:p></p>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in">I
had forgotten about that change. You could
just edit the script and change or even remove
the regexp:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in">foreach
my $line(($_)) {<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in">What's
your Perl version and system architecture? I'm
surprised this has not caught anyone else out.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in">Will<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">On
4 June 2015 at 14:47, Guillermo Marco Puche
<<a moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">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):<o:p></o:p></p>
<pre style="margin-left:.5in"><b> # split again to avoid Windows character nonsense</b><o:p></o:p></pre>
<pre style="margin-left:.5in"><b> foreach my $line(split /\r|\R/) {</b><o:p></o:p></pre>
<p class="MsoNormal" style="margin-left:.5in"><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. <o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><o:p> </o:p></p>
<div>
<p class="MsoNormal"
style="margin-left:.5in">On 04/06/15
15:16, Will McLaren wrote:<o:p></o:p></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<p style="margin-left:.5in">Sorry
Guillermo, I'm running out of ideas. <o:p></o:p></p>
<p style="margin-left:.5in">Does the
test unit run OK?<o:p></o:p></p>
<p style="margin-left:.5in">perl
ensembl-tools/scripts/variant_effect_predictor/t/variant_effect_predictor.t<o:p></o:p></p>
<p style="margin-left:.5in">Will<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="margin-left:.5in">On 4 Jun
2015 12:27, "Guillermo Marco Puche"
<<a moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="margin-left:.5in">Hi Will,<br>
<br>
I'm getting the exact same error
with example_GRCh37.vcf:<o:p></o:p></p>
<pre style="margin-left:.5in">ERROR: Could not detect input file format<o:p></o:p></pre>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><br>
I've made a test script as you
suggest with the following code
and I don't get any error:<o:p></o:p></p>
<pre style="margin-left:.5in">#!/usr/bin/env perl<o:p></o:p></pre>
<pre style="margin-left:.5in"><o:p> </o:p></pre>
<pre style="margin-left:.5in">use strict;<o:p></o:p></pre>
<pre style="margin-left:.5in">use Bio::EnsEMBL::Variation::Utils::VEP qw(detect_format);<o:p></o:p></pre>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><br>
Regards,<br>
Guillermo.<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="margin-left:.5in">On
04/06/15 13:12, Will McLaren
wrote:<o:p></o:p></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<p style="margin-left:.5in">Hi
again<o:p></o:p></p>
<p style="margin-left:.5in">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.<o:p></o:p></p>
<p style="margin-left:.5in">You
could write a short script to
test the method, just import
detect_format from
Bio:EnsEMBL::Variation::Utils::VEP<o:p></o:p></p>
<p style="margin-left:.5in">Does
it detect the example_GRCh37.vcf
format correctly?<o:p></o:p></p>
<p style="margin-left:.5in">The
file you shared on Dropbox works
fine for me on my Mac and a
Linux box.
<o:p></o:p></p>
<p style="margin-left:.5in">Will<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="margin-left:.5in">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:<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">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:<o:p></o:p></p>
<pre style="margin-left:.5in">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<o:p></o:p></pre>
<pre style="margin-left:.5in">2015-06-04 11:36:59 - Starting...<o:p></o:p></pre>
<pre style="margin-left:.5in">ERROR: Could not detect input file format<o:p></o:p></pre>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><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>
<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="margin-left:.5in">On
04/06/15 09:32, Guillermo
Marco Puche wrote:<o:p></o:p></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">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.<o:p></o:p></p>
<pre style="margin-left:.5in"><b>echo $PERL5LIB </b><o:p></o:p></pre>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">/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<o:p></o:p></p>
<pre style="margin-left:.5in"><b>ll /share/gluster/tests/gmarco/tmp</b><o:p></o:p></pre>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">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<o:p></o:p></p>
<pre style="margin-left:.5in"><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><o:p></o:p></pre>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">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.<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="margin-left:.5in">On
03/06/15 18:14, Will
McLaren wrote:<o:p></o:p></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"
style="margin-left:.5in">Hi
again, <o:p></o:p></p>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">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.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">See
commands I used and
input below.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">Perhaps
you haven't got
release/79 of
ensembl-tools too?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">Have
you tried running
the installer from
within
ensembl-tools/scripts/variant_effect_predictor?
This shouldn't
affect your PERL5LIB
or other git
checkouts.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">Will<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">===================<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">mkdir
~/src/tmp<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">cd
~/src/tmp<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">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><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">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><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">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><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">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><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">export
PERL5LIB=ensembl/modules:ensembl-variation/modules:ensembl-funcgen/modules:/Users/will/src/bioperl-1.2.3/:/Users/will/src/lib/perl5/<o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">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<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:09:54 - Starting...<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:09:54 - Detected format of input
file as vcf<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:09:54 - Read 1 variants into
buffer<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:09:54 - Reading transcript data
from cache and/or
database<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">[================================================================================================================================]
[ 100% ]<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:10:00 - Retrieved 7 transcripts
(0 mem, 0 cached,
7 DB, 0
duplicates)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:10:00 - Analyzing chromosome 1<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:10:00 - Analyzing variants<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">[================================================================================================================================]
[ 100% ]<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:10:00 - Calculating consequences<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:10:00 - Processed 1 total
variants (0
vars/sec, 0
vars/sec total)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:10:00 - Wrote stats summary to
variant_effect_output.txt_summary.html<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in">2015-06-03 17:10:00 - Finished!<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
<div>
<p class="MsoNormal"
style="margin-left:.5in">On
3 June 2015 at
16:51, Guillermo
Marco Puche <<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="margin-left:.5in">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. <o:p></o:p></p>
<div>
<div>
<p
class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">
<o:p> </o:p></p>
<div>
<p
class="MsoNormal"
style="margin-left:.5in">On 03/06/15 17:30, Will McLaren wrote:<o:p></o:p></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p
class="MsoNormal"
style="margin-left:.5in">Hi Guille, <o:p></o:p></p>
<div>
<p
class="MsoNormal"
style="margin-left:.5in"><br>
It looks to me
like your
input is not
being parsed
properly.<o:p></o:p></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in">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.<o:p></o:p></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in">If you still have an issue, can you send a line
or two of the
input that
recreates
these issues?<o:p></o:p></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in">Thanks<o:p></o:p></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in">Will McLaren<o:p></o:p></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in">Ensembl Variation<o:p></o:p></p>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
</div>
<div>
<p
class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
<div>
<p
class="MsoNormal"
style="margin-left:.5in">On 3 June 2015 at 16:16, Guillermo Marco Puche
<<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>>
wrote:<o:p></o:p></p>
<div>
<p
class="MsoNormal"
style="margin-left:.5in">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):<o:p></o:p></p>
<p
class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:1.0in;text-indent:-.25in;mso-list:l0
level1 lfo1">
<!--[if !supportLists]--><span
style="font-size:10.0pt;font-family:Symbol"><span
style="mso-list:Ignore">·<span
style="font:7.0pt
"Times
New
Roman"">
</span></span></span><!--[endif]-->git
clone --branch
release/79 <a
moz-do-not-send="true" href="https://github.com/Ensembl/ensembl.git"
target="_blank">
<span
style="color:#5C3566">https://github.com/Ensembl/ensembl.git</span></a>
ensembl_79<o:p></o:p></p>
<p
style="margin-left:.5in">PERL5LIB
env variable
is correctly
pointing to
the cloned
API:
<o:p></o:p></p>
<p
class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:1.0in;text-indent:-.25in;mso-list:l1
level1 lfo2">
<!--[if !supportLists]--><span
style="font-size:10.0pt;font-family:Symbol"><span
style="mso-list:Ignore">·<span
style="font:7.0pt
"Times
New
Roman"">
</span></span></span><!--[endif]-->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<o:p></o:p></p>
<p
style="margin-left:.5in">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.<o:p></o:p></p>
<p
style="margin-left:.5in">I've
been reading
the docs again
and I can't
seen any
additional
PERL library
requirement.<o:p></o:p></p>
<p
style="margin-left:.5in">Here's
the error log:
<a
moz-do-not-send="true"
href="http://pastebin.com/VvQrkEQZ" target="_blank">
http://pastebin.com/VvQrkEQZ</a><o:p></o:p></p>
<p
style="margin-left:.5in"><br>
Thank you!<o:p></o:p></p>
<p
style="margin-left:.5in">Best
regards,<br>
Guille.<o:p></o:p></p>
</div>
<p
class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">
<br>
_______________________________________________<br>
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Ensembl Blog:
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moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p>
</div>
<p
class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<p
class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">
<o:p> </o:p></p>
<pre style="margin-left:.5in">_______________________________________________<o:p></o:p></pre>
<pre style="margin-left:.5in">Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><o:p></o:p></pre>
<pre style="margin-left:.5in">Posting guidelines and subscribe/unsubscribe info: <a moz-do-not-send="true" href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><o:p></o:p></pre>
<pre style="margin-left:.5in">Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></pre>
</blockquote>
<p
class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in">
<o:p> </o:p></p>
</div>
</div>
</div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><br>
_______________________________________________<br>
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Ensembl Blog: <a
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href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p>
</div>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><o:p> </o:p></p>
<pre style="margin-left:.5in">_______________________________________________<o:p></o:p></pre>
<pre style="margin-left:.5in">Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><o:p></o:p></pre>
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<pre style="margin-left:.5in">Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><br>
<br>
<br>
<o:p></o:p></p>
<pre style="margin-left:.5in">_______________________________________________<o:p></o:p></pre>
<pre style="margin-left:.5in">Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><o:p></o:p></pre>
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<pre style="margin-left:.5in">Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><o:p> </o:p></p>
</div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><br>
_______________________________________________<br>
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Ensembl Blog: <a
moz-do-not-send="true"
href="http://www.ensembl.info/"
target="_blank">http://www.ensembl.info/</a><o:p></o:p></p>
</div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><o:p> </o:p></p>
<pre style="margin-left:.5in">_______________________________________________<o:p></o:p></pre>
<pre style="margin-left:.5in">Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><o:p></o:p></pre>
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<pre style="margin-left:.5in">Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></pre>
</blockquote>
</div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><br>
_______________________________________________<br>
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Ensembl Blog: <a
moz-do-not-send="true"
href="http://www.ensembl.info/"
target="_blank">http://www.ensembl.info/</a><o:p></o:p></p>
</div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><o:p> </o:p></p>
<pre style="margin-left:.5in">_______________________________________________<o:p></o:p></pre>
<pre style="margin-left:.5in">Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><o:p></o:p></pre>
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<pre style="margin-left:.5in">Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"
style="margin-left:.5in"><o:p> </o:p></p>
</div>
</div>
</div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><br>
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<p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
</div>
<p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><o:p> </o:p></p>
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