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

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Tue May 14 08:46:23 BST 2013


Hello,

It seems that Conservation plugin on VEP plugin repository has some bugs:

ERROR: Forked process failed

Use of uninitialized value in numeric ge (>=) at /home/likewise-open/SGNET/gmarco/.vep/Plugins/Conservation.pm line 105.

Regards,
Guillermo.

On 05/14/2013 09:28 AM, Guillermo Marco Puche wrote:
> Hello,
>
> I just added the chr5.vcf file that is causing me the crashes to the repo.
> Forget about the weird vcf format. First columns are standard the rest 
> are not.
> https://github.com/guillermomarco/vep_plugins_71/blob/master/chr5.vcf
>
> On 05/14/2013 08:37 AM, Guillermo Marco Puche wrote:
>> Hello,
>>
>> 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.
>>
>> Here are both:
>>
>> https://github.com/guillermomarco/vep_plugins_71
>>
>> 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.
>>
>> 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.
>>
>> Best regards,
>> Guillermo.
>>
>> On 05/13/2013 03:55 PM, Duarte Molha wrote:
>>> 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 
>>> <mailto: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.pm
>>>     for 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
>>>     <mailto: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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