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 <myip@cshl.edu> 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-...

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.

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