[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.
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20130514/f2814318/attachment.html>
More information about the Dev
mailing list