At first we thought it could be an ssh issue but submitting jobs and getting the output back isn't a problem when I do it from my personal user manually, so it's really related to Galaxy. We're using PBS Pro btw. And I'm still at loss... :( L-A Le 23/04/2012 15:42, zhengqiu cai a écrit :
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.schmitt@embl.de> 写道：
发件人: Louise-Amélie Schmitt<louise-amelie.schmitt@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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