On Feb 13, 2012, at 11:07 AM, p.baska...@leeds.ac.uk wrote:

> Hi Nate, 
> 
> I got the following error in the log file after running cufflinks on the 
> local instance of galaxy:
> 

Hi Praveen,

Please use the galaxy-dev mailing list (CC'd) for these types of questions so 
that you can receive a more timely and accurate response.

> galaxy.jobs.runners.drmaa DEBUG 2012-02-13 16:03:26,703 (340/2364848) state 
> change: job is running
> 10.12.152.44 - - [13/Feb/2012:16:03:29 +0100] "POST 
> /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8181/history"; 
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/535.11 (KHTML, 
> like Gecko) Chrome/17.0.963.46 Safari/535.11"
> galaxy.jobs.runners.drmaa DEBUG 2012-02-13 16:03:33,081 (340/2364848) state 
> change: job finished normally
> galaxy.jobs DEBUG 2012-02-13 16:03:33,203 finish(): Could not move 
> /nobackup/galaxy/database/job_working_directory/340/cufflinks_out/genes.fpkm_tracking
>  to /nobackup/galaxy/database/files/000/dataset_397.dat as directed by 
> from_work_dir
> galaxy.jobs DEBUG 2012-02-13 16:03:33,236 finish(): Could not move 
> /nobackup/galaxy/database/job_working_directory/340/cufflinks_out/isoforms.fpkm_tracking
>  to /nobackup/galaxy/database/files/000/dataset_398.dat as directed by 
> from_work_dir
> 10.12.152.44 - - [13/Feb/2012:16:03:34 +0100] "POST 
> /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8181/history"; 
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/535.11 (KHTML, 
> like Gecko) Chrome/17.0.963.46 Safari/535.11"
> 10.12.152.44 - - [13/Feb/2012:16:03:34 +0100] "POST 
> /root/history_get_disk_size HTTP/1.1" 200 - "http://localhost:8181/history"; 
> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/535.11 (KHTML, 
> like Gecko) Chrome/17.0.963.46 Safari/535.11"
> galaxy.jobs DEBUG 2012-02-13 16:03:36,271 job 340 ended
> galaxy.datatypes.metadata DEBUG 2012-02-13 16:03:36,272 Cleaning up external 
> metadata files
> galaxy.datatypes.metadata DEBUG 2012-02-13 16:03:36,489 Failed to cleanup 
> MetadataTempFile temp files from 
> ../../../../../../nobackup/galaxy/database/tmp/metadata_out_HistoryDatasetAssociation_529_nHaLSL:
>  No JSON object could be decoded: line 1 column 0 (char 0)

It looks like the job has failed and what you're seeing here is the failure of 
the job finish/cleanup process since the job failed to produce expected 
outputs.  Try setting cleanup_job = never in your Galaxy config file and then 
have a look at the DRM's output and error files to see if this reveals anything 
about why the job failed.

--nate

> 
> 
> can you please help me to solve this. 
> 
> Thanks 
> Praveen


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