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.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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