<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
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Hello Will,<br>
<br>
I've currently installed Perl 5.14.4 and seems to be working good. I
also tried 5.22(released a few days) but I had a lot of troubles
with many CPAN modules.<br>
<br>
<b>I only get warnings when using local cache (VEP 79 GrCH38 cache)</b>.
Cache is indexed cache with convert_cache.pl script.<br>
I'm trying with both example files provided in ensembl-tools and I'm
getting the following warnings:<br>
<br>
<pre>Argument "-/C" isn't numeric in numeric eq (==) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 5854.</pre>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 08/06/15 10:43, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX3a7nij+mbEK6A8z13eF_2uMWXxVqDdCF0kMGfrrsrs-Q@mail.gmail.com"
type="cite">
<div dir="ltr">This is probably because Perl can't determine the
width of your terminal.
<div><br>
</div>
<div>Nothing to worry about, just use --no_progress and just
pretend you can see animated equals signs moving across your
screen :-)</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 5 June 2015 at 13:51, Guillermo
Marco Puche <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Hi 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I got some of my plugins outdated but that's a totally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>On 05/06/15 14:34, Harpreet Riat wrote:<br>
</div>
<blockquote type="cite">
<div>
<div>Hi Guillermo,</div>
<div><br>
</div>
<div>Can you try replacing that with split /\n/ or
/\n|\r/?</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Harpreet</div>
</div>
<div>
<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>
<div> 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><a moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a>
-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 <a moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a>
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>\v</span><span
style="color:windowtext"> and
</span><span>\h</span><span
style="color:windowtext">
escapes that match vertical
and horizontal whitespace,
respectively. </span><span>\V</span><span
style="color:windowtext"> and
</span><span>\H</span><span
style="color:windowtext">
logically match their
complements.</span></p>
<p style="margin:0px"> <span>\R</span><span
style="color:windowtext">
matches a generic linebreak,
that is, vertical whitespace,
plus the multi-character
sequence </span><span>"\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>
</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>
</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>
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<pre>_______________________________________________
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_______________________________________________<br>
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href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
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<pre wrap="">_______________________________________________
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