[ensembl-dev] VEP error: Forked process failed.

[Duarte Molha]

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.

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.

Cheers

Duarte

=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================


On Mon, May 13, 2013 at 2:50 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Guillermo,
>
> 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.
>
> 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.
>
> 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
> https://github.com/ensembl-variation/VEP_plugins/blob/master/ProteinSeqs.pmfor an example.
>
> If you still have no luck, send me the code and an input file that
> recreates the problem.
>
> Regards
>
> Will
>
>
> On 13 May 2013 13:18, Guillermo Marco Puche <
> guillermo.marco at sistemasgenomicos.com> wrote:
>
>>  Hello,
>>
>> I've started to recently having problems with VEP script while using
>> different plugins (most of them own plugins).
>>
>> 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
>>
>>
>>
>> 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.
>>
>> I'm running VEP on verbose mode but I can't get any usefull information.
>> How could I debug that?
>>
>> Best regards,
>> Guillermo.
>>
>>
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