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
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