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" <nate@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

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