On Jan 31, 2012, at 5:29 AM, Praveen Baskaran wrote: > Nate, > > Thanks, > I have already changed that in unververse_wsgi.ini, but the problem > continues. > > When I checked the galaxy.log file after executing samtools, got the > following error: > > > > galaxy.jobs.runners.drmaa DEBUG 2012-01-28 16:14:18,582 (258/2349769) > state change: job is running > > galaxy.jobs.runners.drmaa DEBUG 2012-01-28 16:14:20,174 (258/2349769) > state change: job finished normally > > galaxy.datatypes.metadata DEBUG 2012-01-28 16:14:20,405 loading metadata > from file for: HistoryDatasetAssociation 412 > > 10.12.152.44 - - [28/Jan/2012:16:14:20 +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/535.7 (KHTML, > like Gecko) Chrome/16.0.912.77 Safari/535.7" > > galaxy.jobs.runners.drmaa ERROR 2012-01-28 16:14:20,755 Job wrapper finish > method failed > > Traceback (most recent call last): > > File > "/apps1/applications/galaxy/galaxy-dist/1/default/lib/galaxy/jobs/runners/d > rmaa.py", line 282, in finish_job > > drm_job_state.job_wrapper.finish( stdout, stderr ) > > File > "/apps1/applications/galaxy/galaxy-dist/1/default/lib/galaxy/jobs/__init__. > py", line 569, in finish > > dataset.metadata.from_JSON_dict( > self.external_output_metadata.get_output_filenames_by_dataset( dataset, > self.sa_session ).filename_out ) > > File > "/apps1/applications/galaxy/galaxy-dist/1/default/lib/galaxy/datatypes/meta > data.py", line 109, in from_JSON_dict > > dataset._metadata[ name ] = spec.param.from_external_value( > JSONified_dict[ name ], dataset ) > > File > "/apps1/applications/galaxy/galaxy-dist/1/default/lib/galaxy/datatypes/meta > data.py", line 440, in from_external_value > > shutil.move( value.file_name, mf.file_name ) > > File > "/apps1/applications/galaxy/galaxy-dist/1/default/lib/galaxy/model/__init__ > .py", line 1601, in file_name > > os.makedirs( path ) > > File "/apps/compilers/python/2.7.2/2/default/lib/python2.7/os.py", line > 157, in makedirs > > mkdir(name, mode) > > OSError: [Errno 13] Permission denied: > '/nobackup/galaxy/database/files/_metadata_files/000'.
Hi Praveen, It looks like the file_path directory (in this case the default <galaxy root>/database/files/) is not writable by the user running Galaxy. --nate > > > > > > Thanks > > Praveen Baskaran > > > > > > > On 30/01/2012 17:43, "Nate Coraor" <n...@bx.psu.edu> wrote: > >> On Jan 25, 2012, at 5:28 AM, Praveen Baskaran wrote: >> >>> i have installed local instance of galaxy and have a small problem with >>> samtools. when i try to convert sam file to bam, the result pane shows >>> that the job is running (for several hours). but when check the galaxy >>> log file, it shows that the job is finished normally. i can also find >>> the result (bam) file in galaxy/database/files/000/ folder. can anyone >>> help to resolve this issue. >> >> Hi Praveen, >> >> Please change the following in your universe_wsgi.ini: >> >> set_metadata_externally = True >> >> And let us know if this makes a difference. Most likely, the tool output >> is very large and the Galaxy process is setting metadata on it. With >> metadata set externally, you'll be able to see this step as a separate >> process. >> >> --nate >> >>> >>> 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/ > > ___________________________________________________________ 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/
