<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 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 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 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 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>
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