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<div class="moz-cite-prefix">Hello,<br>
<br>
It seems that Conservation plugin on VEP plugin repository has
some bugs:<br>
<br>
<pre>ERROR: Forked process failed</pre>
<pre>Use of uninitialized value in numeric ge (>=) at /home/likewise-open/SGNET/gmarco/.vep/Plugins/Conservation.pm line 105.
</pre>
Regards,<br>
Guillermo.<br>
<br>
On 05/14/2013 09:28 AM, Guillermo Marco Puche wrote:<br>
</div>
<blockquote cite="mid:5191E785.1010704@sistemasgenomicos.com"
type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<div class="moz-cite-prefix">Hello,<br>
<br>
I just added the chr5.vcf file that is causing me the crashes to
the repo.<br>
Forget about the weird vcf format. First columns are standard
the rest are not.<br>
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<a moz-do-not-send="true"
href="https://github.com/guillermomarco/vep_plugins_71/blob/master/chr5.vcf">https://github.com/guillermomarco/vep_plugins_71/blob/master/chr5.vcf</a><br>
<br>
On 05/14/2013 08:37 AM, Guillermo Marco Puche wrote:<br>
</div>
<blockquote cite="mid:5191DBB1.1060509@sistemasgenomicos.com"
type="cite">
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<div class="moz-cite-prefix">Hello,<br>
<br>
I'm not really sure which one of those plugins is causing the
fork error. I cannot recreate it now running each one of them
separately.<br>
<br>
Here are both:<br>
<br>
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<a moz-do-not-send="true"
href="https://github.com/guillermomarco/vep_plugins_71">https://github.com/guillermomarco/vep_plugins_71</a><br>
<br>
They also slow the calculating consequences process a lot.
aa_grantham_distance.pm is just a hardcoded plugin from one of
the biologists in my work. It was just a pure copy paste and
adaptation to make it work as a VEP plugin. Maybe the problem
is in the matrix definition every time the sub routine is
called. I'm not running out of memory nor CPU. I'm currently
using it with 2 threads and buffersize of 500 for a 5000
variant vcf file.<br>
<br>
I'm my honest opinion, I think one (or even both) of those
plugins are slowing so much the calculating process that
sometimes the fork just dies. Like when you have a timeout
during to heavy network traffic. So when you use them together
with lot of other plugins like Condel, Consequence, etc.. they
may be causing the process to handle and die.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 05/13/2013 03:55 PM, Duarte Molha wrote:<br>
</div>
<blockquote
cite="mid:CAGqkoE+MjhwtB4nVk9kF6Ah0SMU9jg-VDC9nMLfsm63OvOedLg@mail.gmail.com"
type="cite">
<div dir="ltr">I also get this error... it is so prevalent and
so difficult to pinpoint what is causing it that I have
given up on forking my annotation process.
<div><br>
</div>
<div>I do think it is related to the number of forks. It
seems to crash less often if you use a low number of
forks... anything above 5 will undoubtedly crash the
script at least in my experience.</div>
<div><br>
</div>
<div style="">Cheers</div>
<div style=""><br>
Duarte</div>
</div>
<div class="gmail_extra"><br clear="all">
<div><font style="background-color:rgb(255,255,255)"
color="#999999">=========================<br>
Duarte Miguel Paulo Molha <br>
</font>
<div><font style="background-color:rgb(255,255,255)"
color="#999999"> <a moz-do-not-send="true"
href="http://about.me/duarte" target="_blank">http://about.me/duarte</a>
<br>
=========================</font></div>
</div>
<br>
<br>
<div class="gmail_quote">On Mon, May 13, 2013 at 2:50 PM,
Will McLaren <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:wm2@ebi.ac.uk"
target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>Test each plugin individually until you find the
one that causes the error. It is highly unlikely
that a particular combination of plugins is causing
the crash.</div>
<div><br>
</div>
<div>Check that there are no "print" (to STDOUT or
STDERR) statements in your plugin - forking assumes
that code remains silent otherwise it will throw
errors like this.</div>
<div><br>
</div>
<div> Also, check what, if anything, is cached between
runs of your plugin. If you are caching things (for
example to avoid re-querying a database), you may
need to write storable hooks to ensure the data is
getting cached between forks - see <a
moz-do-not-send="true"
href="https://github.com/ensembl-variation/VEP_plugins/blob/master/ProteinSeqs.pm"
target="_blank">https://github.com/ensembl-variation/VEP_plugins/blob/master/ProteinSeqs.pm</a>
for an example.</div>
<div><br>
</div>
<div>If you still have no luck, send me the code and
an input file that recreates the problem.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"> <br>
<br>
<div class="gmail_quote">
<div>
<div class="h5">On 13 May 2013 13:18, 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>
</div>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div class="h5">
<div bgcolor="#FFFFFF" text="#000066"> Hello,<br>
<br>
I've started to recently having problems
with VEP script while using different
plugins (most of them own plugins).<br>
<br>
<pre>2013-05-13 13:59:44 - Connected to core version 71 database and variation version 71 database
2013-05-13 13:59:44 - Loaded plugin: vcf_input
2013-05-13 13:59:44 - Loaded plugin: biobase
2013-05-13 13:59:44 - Loaded plugin: aa_grantham_distance
2013-05-13 13:59:44 - Loaded plugin: flanking_sequence
2013-05-13 13:59:44 - Loaded plugin: Condel
2013-05-13 13:59:44 - Output fields redefined (37 defined)
2013-05-13 13:59:44 - Starting...
2013-05-13 13:59:45 - Read 3888 variants into buffer
2013-05-13 13:59:54 - Reading transcript data from cache and/or database
[===============================================] [ 100% ]
2013-05-13 14:02:38 - Retrieved 6463 transcripts (0 mem, 0 cached, 13743 DB, 7280 duplicates)
2013-05-13 14:02:38 - Calculating consequences
[===================================> ] [ 78% ]
ERROR: Forked process failed
</pre>
I'm not getting any other error message. So
I cannot debug properly. I thought my
plugins were OK but it's seems they don't. I
think the problem occurs when I use
"aa_grantham_distance plugin" together with
"flanking_sequence". I've no idea what could
be causing this.<br>
<br>
I'm running VEP on verbose mode but I can't
get any usefull information. How could I
debug that?<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
</div>
<br>
</div>
</div>
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