Job output not returned from Cluster Error

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Job output not returned from Cluster Error

Yip, Miu ki
Hi,

We’re having a bit of an error where the GUI shows that a job had an error. When the user submits the job, the job is seen to have run via terminal and uge. The job working directory exists and the out and error file is in there. Once the job completes, it seems like the GUI will say that it works. But then several minutes later, the GUI shows the job turning from green to red and giving the error that the “Job output not returned from the Cluster” error.

I tried setting the retry_job_output_collection but it did not work (we’re using a local file system): http://dev.list.galaxyproject.org/Problem-related-to-a-job-that-quot-failed-quot-td4627406.html#a4632168

This seems to happen randomly for different jobs. Some jobs receive errors but others do not receive this error.

Does anybody have any suggestions on how to fix this? There is no error that appears in the paster.log file and we are using SGE.

Thanks in advance!
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Re: Job output not returned from Cluster Error

Devon Ryan-2
Presuming SGE runs this on a remote node, it's likely the file hasn't been flushed to disk. Have you checked to see if the files eventually show up?

Sent from my iPhone

> On 17. Aug 2017, at 17:49, Yip, Miu ki <[hidden email]> wrote:
>
> Hi,
>
> We’re having a bit of an error where the GUI shows that a job had an error. When the user submits the job, the job is seen to have run via terminal and uge. The job working directory exists and the out and error file is in there. Once the job completes, it seems like the GUI will say that it works. But then several minutes later, the GUI shows the job turning from green to red and giving the error that the “Job output not returned from the Cluster” error.
>
> I tried setting the retry_job_output_collection but it did not work (we’re using a local file system): http://dev.list.galaxyproject.org/Problem-related-to-a-job-that-quot-failed-quot-td4627406.html#a4632168
>
> This seems to happen randomly for different jobs. Some jobs receive errors but others do not receive this error.
>
> Does anybody have any suggestions on how to fix this? There is no error that appears in the paster.log file and we are using SGE.
>
> Thanks in advance!
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/