I am having the same problem when I use condor as the scheduler instead of sge.

Cai

--- 12年4月23日,周一, Louise-Amélie Schmitt <louise-amelie.schm...@embl.de> 写道:

> 发件人: Louise-Amélie Schmitt <louise-amelie.schm...@embl.de>
> 主题: [galaxy-dev] Error: Job output not returned from cluster
> 收件人: galaxy-dev@lists.bx.psu.edu
> 日期: 2012年4月23日,周一,下午5:09
> Hello everyone,
> 
> I'm still trying to set up the job submission as the real
> user, and I get a mysterious error. The job obviously runs
> somewhere and when it ends it is in error state and displays
> the following message: "Job output not returned from
> cluster"
> 
> In the Galaxy log I have the following lines when the job
> finishes running:
> 
> galaxy.jobs.runners.drmaa DEBUG 2012-04-23 10:36:41,509
> (1455/9161620.pbs-master2.embl.de) state change: job
> finished, but failed
> galaxy.jobs.runners.drmaa DEBUG 2012-04-23 10:36:41,511 Job
> output not returned from cluster
> galaxy.jobs DEBUG 2012-04-23 10:36:41,547 finish(): Moved
> /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/galaxy_dataset_2441.dat
> to
> /g/funcgen/galaxy-dev/database/files/002/dataset_2441.dat
> galaxy.jobs DEBUG 2012-04-23 10:36:41,755 job 1455 ended
> galaxy.datatypes.metadata DEBUG 2012-04-23 10:36:41,755
> Cleaning up external metadata files
> galaxy.datatypes.metadata DEBUG 2012-04-23 10:36:41,768
> Failed to cleanup MetadataTempFile temp files from
> /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/metadata_out_HistoryDatasetAssociation_1606_npFIJM:
> No JSON object could be decoded: line 1 column 0 (char 0)
> 
> The
> /g/funcgen/galaxy-dev/database/job_working_directory/001/1455/
> directory is empty and
> /g/funcgen/galaxy-dev/database/files/002/dataset_2441.dat
> exists but is empty.
> 
> Any ideas about what can go wrong there? Any lead would be
> immensely appreciated!
> 
> Thanks,
> L-A
> 
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