On Feb 13, 2012, at 11:07 AM, P.Baskaran@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