Hi Hans-Rudolf.

Yes, I have this error in my log file :"MySQL server has gone away"!!!
So I changed the option database_engine_option_pool and it seems to work fine!

Thanks a lot for your help.

And for the information, when a job is queued on a local instance not
in a cluster, when we restart the server, the job is crashed to the
error state.

Thanks again.

julie

2014-07-23 14:25 GMT+02:00 Hans-Rudolf Hotz <h...@fmi.ch>:
>
>
> On 07/23/2014 02:13 PM, julie dubois wrote:
>>
>> I'm using a MySQL database !!!
>> But may be such database-lock can appear because of my universe.ini
>> configuration file.
>> Here it's the lines concerning the database :
>>
>> database_engine_option_pool_size = 10
>> database_engine_option_max_overflow = 20
>> database_engine_option_pool_recycle = -1
>> database_engine_option_strategy = threadlocal
>>
>>
>> Can one of these parameters be at the origin of my problem ?
>>
>
>
> we are also using MySQL, but we use the suggested setting:
>
> database_engine_option_pool_recycle = 7200
>
>
> though, i don't think this is related to your problem. Or did you get the
> error: "MySQL server has gone away" in the galaxy log file?
>
>
>
>>
>> If yes, when I'll restart Galaxy, the queued jobs will be in a staying
>> state with the capacity to become in a running state ?
>> Or they will be in error state and I should restart the process as new
>> jobs ?
>
>
> I don't know, I don't have enough experience with queued workflow jobs and
> what is happening with them during a re-start. I am sorry, I can't be of
> much further help.  Maybe someone else on the list?
>
> Hans-Rudolf
>
>
>
>
>>
>>
>> Thanks.
>>
>> Julie
>>
>> 2014-07-23 12:55 GMT+02:00 Hans-Rudolf Hotz <h...@fmi.ch>:
>>>
>>>
>>>
>>> On 07/23/2014 12:05 PM, julie dubois wrote:
>>>>
>>>>
>>>> Hi Hans-Rudolf,
>>>> Thanks for your answer.
>>>> I've launched lot of jobs since monday. And some jobs were finished
>>>> and some jobs never started.
>>>> In "Manage jobs" I can see jobs queued because they need inputs which
>>>> are queued, so I think it's normal.
>>>>
>>>> But other jobs are described like this :
>>>>
>>>> 9554   user_login   0 hours ago    samtools_flagstat    new    23199
>>>> ok, 23243 ok    None    None    None
>>>> The two necessary inputs for this job (23199 and 2343) are ok and the
>>>> job doesn't run.
>>>>
>>>>
>>>> Another mysterious line is :
>>>>
>>>> 9561  user_login    0 hours ago     fastqc       new      Unable to
>>>> determine inputs      None     None    None
>>>>
>>>> After check this job in my history, I'm sure that the input of this
>>>> job is green and really available. Why can galaxy not determine inputs
>>>> ?
>>>> Finally, in "Manage Jobs" there are only jobs queued. No jobs running.
>>>>
>>>> Any idea ?
>>>
>>>
>>>
>>> I have one suspicion:
>>>
>>> which database are you using?
>>> If you are just using the built in SQlite you might have run in a
>>> database-lock?  Because you have submitted too many jobs at once?
>>>
>>> In this case, I guess, the only way to recover is to re-start...
>>>
>>> Hans-Rudolf
>>>
>>>
>>>
>>>> Thanks
>>>> Julie
>>>>
>>>> 2014-07-23 11:35 GMT+02:00 Hans-Rudolf Hotz <h...@fmi.ch>:
>>>>>
>>>>>
>>>>> Hi Julie
>>>>>
>>>>> Are there any jobs running at all?  What do you get when you click on
>>>>> "Manage jobs" in the admin menu?  Maybe you have some old jobs
>>>>> 'running'
>>>>> which are now blocking your queue?
>>>>>
>>>>> Hans-Rudolf
>>>>>
>>>>>
>>>>>
>>>>> On 07/23/2014 11:14 AM, julie dubois wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> Hi all,
>>>>>> I've seen several posts for jobs which stay queued and never start
>>>>>> with an installation of galaxy on a cluster.
>>>>>> But our installation is just a local instance of galaxy in 1 PC and I
>>>>>> have more than 100 jobs which stay queued and never start.
>>>>>>
>>>>>> How can I debug this problem (my version of galaxy is the latest
>>>>>> 2june2014).
>>>>>>
>>>>>> And is it possible to run those jobs without restart galaxy because it
>>>>>> would be very long to rerun each job manually after reloading galaxy.
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> Julie
>>>>>> ___________________________________________________________
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>>>>>>
>>>>>
>>>
>
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