Hmm.
This could be related to the problem Bjoern recently reported,
which Nate says was partly addressed in a recent fix:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-February/018367.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-February/018382.html
What version of Galaxy do you have Ravi (i.e. what hg revision,
find out by running "hg summary" at the command line)?
Peter
On Wed, Feb 26, 2014 at 2:22 PM, Sanka, Ravi wrote:
> Hi Peter,
>
> This galaxy instance is connected to our SGE, and all jobs get run on it.
> When we started this particular job, and it was the only job running, 4 of
> the 10 tasks it was split to were able to run simultaneously, which we
> viewed with qstat.
>
> But after those four completed successfully, qstat revealed nothing
> running, not even the original job. The Galaxy front-end interface still
> displayed the job as running.
>
> --
> Ravi Sanka
> ICS Sr. Bioinformatics Engineer
> J. Craig Venter Institute
> 301-795-7743
> --
>
>
>
>
> On 2/25/14 6:21 PM, "Peter Cock" wrote:
>
>>On Tue, Feb 25, 2014 at 10:57 PM, Sanka, Ravi wrote:
>>> Greetings,
>>>
>>> We are trying to enable job-splitting and merging on our Galaxy blast
>>>tools.
>>> We set the following parameters in the universe_wsgi.ini:
>>>
>>> use_tasked_jobs = True
>>> local_task_queue_workers = 2
>>>
>>> Then we executed the tool "NCBI BLAST+ blastn" (from devteam's NCBI
>>>BLAST+)
>>> on a query set of 10,000 sequences. The tool's xml has the following
>>> parallelism tag:
>>>
>>> And as expected, the job was split into 10 tasks (IDs 0-9), each one
>>>with
>>> 1000 sequences. Four tasks started running simultaneously.
>>>
>>> Those four tasks have completed, but now there is no indication that the
>>> other 6 tasks have begun running, and the job on the GUI is still in the
>>> yellow-state in History.
>>>
>>> It has been nearly an hour, and still no sign of those tasks or any job
>>> running. What could be the cause of this?
>>>
>>
>>Is this connected to a cluster (e.g. SGE), or all on one machine?
>>
>>We run this with a cluster, so you can use the cluster tools to
>>monitor the sub-tasks Galaxy created.
>>
>>Peter
>>
>>RE: https://github.com/peterjc/galaxy_blast/issues/35 and
>>http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
>
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