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

[Will McLaren]

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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