<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body text="#000066" bgcolor="#FFFFFF">
Hi Harpreet,<br>
<br>
I've instead updated Perl to latest version.<br>
I got some of my plugins outdated but that's a totally different and
independent problem.<br>
<br>
I'm getting this warning when executing vep script without "<b>--no_progress</b>"
option:<br>
<br>
Negative repeat count does nothing at
/share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
line 6247, <GEN0> line 134.<br>
<br>
Now I'm in a hurry I'll try \n in split on Monday and report back.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 05/06/15 14:34, Harpreet Riat wrote:<br>
</div>
<blockquote cite="mid:02C9E292F0AF4ABF916CAD756507D640@ebi.ac.uk"
type="cite">
<div id="reply-content">
<div id="reply-content">Hi Guillermo,</div>
<div id="reply-content"><br>
</div>
<div id="reply-content">Can you try replacing that with split
/\n/ or /\n|\r/?</div>
<div id="reply-content"><br>
</div>
<div id="reply-content">Thanks,</div>
<div id="reply-content">Harpreet</div>
</div>
<div id="07C342C156484D8C970265870C363F6A">
<div><br>
</div>
</div>
<p style="color: #A0A0A8;">On Friday, 5 June 2015 at 11:36,
Guillermo Marco Puche wrote:</p>
<blockquote type="cite"
style="border-left-style:solid;border-width:1px;margin-left:0px;padding-left:10px;">
<div id="quoted-message-content">
<div>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
Hello Will,<br>
<br>
Thank you for the info Matthew.<br>
<br>
I'm still getting lines split on my work environment.<br>
<br>
<ol>
<li><b>foreach my $line(split /\r|(?>\v|\x0D\x0A)/)
{...}</b><br>
<blockquote>variant_effect_predictor.pl -database -i
input.vcf -o test.vcf --force_overwrite<br>
2015-06-05 12:26:14 - Starting...<br>
<b><font color="#ff0000">4.2</font></b>
("##fileformat=VCFv4.2 getting" split into "<b>4.2</b>"
I putted a print in VEP.pm)<br>
2015-06-05 12:26:14 - Detected format of input file as
id<br>
</blockquote>
</li>
<li><b>foreach my $line(split /(?>\v|\x0D\x0A)/) {...}</b><br>
<blockquote>same result as 1</blockquote>
</li>
<li><b>foreach my $line(split /\r/) {...}<br>
</b>
<blockquote>same result as 1 and 2</blockquote>
</li>
</ol>
I cannot update Perl version at this moment so I gues I will
have to completely remove this split from
variant_effect_predictor.pl code.<br>
How can I update this line of code (176) to avoid any split?<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<br>
<div>On 05/06/15 10:28, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div>
<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><br>
<div>On 4 June 2015 at 19:17, Healy, Matthew <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:Matthew.Healy@bms.com"
target="_blank">Matthew.Healy@bms.com</a>></span>
wrote:<br>
<blockquote type="cite">
<div>
<div bgcolor="white" link="blue" vlink="purple"
lang="EN-US">
<div>
<p style="margin: 0px;"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p style="margin: 0px;"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">The
\R was added in Perl 5.10.0:</span></p>
<p style="margin: 0px;"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><a
moz-do-not-send="true"
href="http://perldoc.perl.org/5.10.0/perldelta.html"
target="_blank">http://perldoc.perl.org/5.10.0/perldelta.html</a></span></p>
<p style="margin: 0px;"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p style="margin: 0px;"><b><span
style="color:windowtext">Vertical and
horizontal whitespace, and linebreak</span></b><span
style="color:windowtext"> </span></p>
<p style="margin: 0px;"> <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.</span></p>
<p style="margin: 0px;"> <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"> .</span></p>
<p style="margin: 0px;"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p style="margin: 0px;"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p style="margin: 0px;"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<div>
<div style="border:none;border-top:solid
#b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p style="margin: 0px;"><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 moz-do-not-send="true"
href="mailto:dev-bounces@ensembl.org"
target="_blank">dev-bounces@ensembl.org</a>
[mailto:<a moz-do-not-send="true"
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
moz-do-not-send="true"
href="mailto:dev@ensembl.org"
target="_blank">dev@ensembl.org</a></span></p>
<div>
<div><br>
<b>Subject:</b> Re: [ensembl-dev]
VEP 79 API problems</div>
</div>
</div>
</div>
<div>
<div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">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:</p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<p style="margin: 0px;"><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></p>
<p style="margin: 0px;"><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"
target="_blank">http://perldoc.perl.org/5.8.8/perlre.html</a></span></p>
<p style="margin: 0px;"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<p style="margin: 0px;"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span></p>
<div
style="border:none;border-top:solid
#b5c4df 1.0pt;padding:3.0pt 0in 0in
0in">
<p style="margin: 0px;"><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 moz-do-not-send="true"
href="mailto:dev-bounces@ensembl.org"
target="_blank">dev-bounces@ensembl.org</a>
[<a moz-do-not-send="true"
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></p>
</div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">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.</p>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">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"
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.</p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">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/"
target="_blank">http://perlbrew.pl/</a></p>
</div>
<div>
<p style="margin: 0px;"> </p>
</div>
<div>
<p style="margin: 0px;">Will</p>
</div>
</div>
<div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">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:</p>
<div>
<p style="margin: 0px;">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 ?</p>
<pre style="margin-left:1.0in"><b> foreach my $line(split /\r|\R/) {</b></pre>
<p style="margin: 0px;"><br>
I was thinking about just
removing \R from regex.<br>
<br>
Regards,<br>
Guillermo.</p>
<div>
<div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin: 0px;">On
04/06/15 17:49, Will
McLaren wrote:</p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p style="margin: 0px;">Thanks
</p>
<div>
<p style="margin:
0px;"> </p>
</div>
<div>
<p style="margin:
0px;">I had
forgotten about that
change. You could
just edit the script
and change or even
remove the regexp:</p>
</div>
<div>
<p style="margin:
0px;"> </p>
</div>
<div>
<p style="margin:
0px;">foreach my
$line(($_)) {</p>
</div>
<div>
<p style="margin:
0px;"> </p>
</div>
<div>
<p style="margin:
0px;">What's your
Perl version and
system architecture?
I'm surprised this
has not caught
anyone else out.</p>
</div>
<div>
<p style="margin:
0px;"> </p>
</div>
<div>
<p style="margin:
0px;">Will</p>
</div>
</div>
<div>
<p style="margin: 0px;"> </p>
<div>
<p style="margin:
0px;">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:</p>
<div>
<p style="margin:
0px;"> 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):</p>
<pre style="margin-left:1.0in"><b> # split again to avoid Windows character nonsense</b></pre>
<pre style="margin-left:1.0in"><b> foreach my $line(split /\r|\R/) {</b></pre>
<p style="margin:
0px;"><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. </p>
<div>
<div>
<p
style="margin:
0px;"> </p>
<div>
<p
style="margin:
0px;">On
04/06/15
15:16, Will
McLaren wrote:</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. </p>
<p
style="margin-left:1.0in">Does
the test unit
run OK?</p>
<p
style="margin-left:1.0in">perl
ensembl-tools/scripts/variant_effect_predictor/t/variant_effect_predictor.t</p>
<p
style="margin-left:1.0in">Will</p>
<div>
<p
style="margin:
0px;">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:</p>
<div>
<p
style="margin:
0px;">Hi Will,<br>
<br>
I'm getting
the exact same
error with
example_GRCh37.vcf:</p>
<pre style="margin-left:1.0in">ERROR: Could not detect input file format</pre>
<p
style="margin:
0px;"> <br>
I've made a
test script as
you suggest
with the
following code
and I don't
get any error:</p>
<pre style="margin-left:1.0in">#!/usr/bin/env perl</pre>
<pre style="margin-left:1.0in"> </pre>
<pre style="margin-left:1.0in">use strict;</pre>
<pre style="margin-left:1.0in">use Bio::EnsEMBL::Variation::Utils::VEP qw(detect_format);</pre>
<p
style="margin:
0px;"> <br>
Regards,<br>
Guillermo.</p>
<div>
<p
style="margin:
0px;">On
04/06/15
13:12, Will
McLaren wrote:</p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<p
style="margin-left:1.0in">Hi
again</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.</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</p>
<p
style="margin-left:1.0in">Does
it detect the
example_GRCh37.vcf
format
correctly?</p>
<p
style="margin-left:1.0in">The
file you
shared on
Dropbox works
fine for me on
my Mac and a
Linux box. </p>
<p
style="margin-left:1.0in">Will</p>
<div>
<p
style="margin:
0px;">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:</p>
<div>
<p
style="margin:
0px;"> 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:</p>
<pre style="margin-left:1.0in">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</pre>
<pre style="margin-left:1.0in">2015-06-04 11:36:59 - Starting...</pre>
<pre style="margin-left:1.0in">ERROR: Could not detect input file format</pre>
<p
style="margin:
0px;"> <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>
</p>
<div>
<p
style="margin:
0px;">On
04/06/15
09:32,
Guillermo
Marco Puche
wrote:</p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<p
style="margin:
0px;"> 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.</p>
<pre style="margin-left:1.0in"><b>echo $PERL5LIB </b></pre>
<p
style="margin:
0px;">
/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</p>
<pre style="margin-left:1.0in"><b>ll /share/gluster/tests/gmarco/tmp</b></pre>
<p
style="margin:
0px;"> 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</p>
<pre style="margin-left:1.0in"><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>
<p
style="margin:
0px;">
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.</p>
<div>
<p
style="margin:
0px;">On
03/06/15
18:14, Will
McLaren wrote:</p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p
style="margin:
0px;">Hi
again, </p>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">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.</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">See
commands I
used and input
below.</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">Perhaps
you haven't
got release/79
of
ensembl-tools
too?</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">Have you
tried running
the installer
from within
ensembl-tools/scripts/variant_effect_predictor?
This shouldn't
affect your
PERL5LIB or
other git
checkouts.</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">Will</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">===================</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">mkdir
~/src/tmp</p>
</div>
<div>
<p
style="margin:
0px;">cd
~/src/tmp</p>
</div>
<div>
<p
style="margin:
0px;">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></p>
</div>
<div>
<p
style="margin:
0px;">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></p>
</div>
<div>
<p
style="margin:
0px;">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></p>
</div>
<div>
<p
style="margin:
0px;">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></p>
</div>
<div>
<p
style="margin:
0px;">export
PERL5LIB=ensembl/modules:ensembl-variation/modules:ensembl-funcgen/modules:/Users/will/src/bioperl-1.2.3/:/Users/will/src/lib/perl5/</p>
</div>
<div>
<div>
<p
style="margin:
0px;">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</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:09:54 -
Starting...</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:09:54 -
Detected
format of
input file as
vcf</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:09:54 -
Read 1
variants into
buffer</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:09:54 -
Reading
transcript
data from
cache and/or
database</p>
</div>
<div>
<p
style="margin:
0px;">[================================================================================================================================]
[ 100% ]</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:10:00 -
Retrieved 7
transcripts (0
mem, 0 cached,
7 DB, 0
duplicates)</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:10:00 -
Analyzing
chromosome 1</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:10:00 -
Analyzing
variants</p>
</div>
<div>
<p
style="margin:
0px;">[================================================================================================================================]
[ 100% ]</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:10:00 -
Calculating
consequences</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:10:00 -
Processed 1
total variants
(0 vars/sec, 0
vars/sec
total)</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:10:00 -
Wrote stats
summary to
variant_effect_output.txt_summary.html</p>
</div>
<div>
<p
style="margin:
0px;">2015-06-03
17:10:00 -
Finished!</p>
</div>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
</div>
<div>
<p
style="margin:
0px;"> </p>
<div>
<p
style="margin:
0px;">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:</p>
<div>
<p
style="margin:
0px;">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. </p>
<div>
<div>
<p
style="margin:
0px;"> </p>
<div>
<p
style="margin:
0px;">On
03/06/15
17:30, Will
McLaren wrote:</p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p
style="margin:
0px;">Hi
Guille, </p>
<div>
<p
style="margin:
0px;"><br>
It looks to me
like your
input is not
being parsed
properly.</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">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.</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">If you
still have an
issue, can you
send a line or
two of the
input that
recreates
these issues?</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">Thanks</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
<div>
<p
style="margin:
0px;">Will
McLaren</p>
</div>
<div>
<p
style="margin:
0px;">Ensembl
Variation</p>
</div>
<div>
<p
style="margin:
0px;"> </p>
</div>
</div>
<div>
<p
style="margin:
0px;"> </p>
<div>
<p
style="margin:
0px;">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:</p>
<div>
<p
style="margin:
0px;">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):</p>
<p
style="margin:
0px;"> <span
style="font-size:10.0pt;font-family:Symbol"><span>·<span
style="font:7.0pt
"Times
New
Roman"">
</span></span></span>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</p>
<p
style="margin-left:1.0in">PERL5LIB
env variable
is correctly
pointing to
the cloned
API: </p>
<p
style="margin:
0px;"> <span
style="font-size:10.0pt;font-family:Symbol"><span>·<span
style="font:7.0pt
"Times
New
Roman"">
</span></span></span>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</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.</p>
<p
style="margin-left:1.0in">I've
been reading
the docs again
and I can't
seen any
additional
PERL library
requirement.</p>
<p
style="margin-left:1.0in">Here's
the error log:
<a
moz-do-not-send="true"
href="http://pastebin.com/VvQrkEQZ" target="_blank">
http://pastebin.com/VvQrkEQZ</a></p>
<p
style="margin-left:1.0in"><br>
Thank you!</p>
<p
style="margin-left:1.0in">Best
regards,<br>
Guille.</p>
</div>
<p
style="margin:
0px;"> <br>
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