I'm using a MySQL database !!!
But may be such database-lock can appear because of my universe.ini
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 ?
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 ?
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...
>> 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?
>>> 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
>>>> 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.
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