On Feb 13, 2012, at 11:07 AM, [email protected] 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
