Check the permissions of the test.bam file. Maybe the galaxy user can't write into a temp directory when it runs the external_chown_script.

On 11/11/2011 3:30 PM, Chorny, Ilya wrote:

When I try to link file paths into a shared data library from the admin menu it fails. I get the following in the log file:

galaxy.jobs DEBUG 2011-11-11 13:24:38,280 (2645) Changing ownership of working directory with: /usr/bin/sudo -E /home/galaxy/production/Sept06/galaxy-central/sc ripts/external_chown_script.py ./database/job_working_directory/2645 galaxy 504

galaxy.jobs ERROR 2011-11-11 13:24:38,771 fail(): Missing output file in working directory:

[Errno 13] Permission denied: '/bioinfoSD/ichorny/test.bam'

galaxy.datatypes.metadata DEBUG 2011-11-11 13:24:38,919 Cleaning up external metadata files

STDOUT has the following :

Job 2645's output dataset(s) could not be read

Also my file get erased:

/bioinfoSD/ichorny/test.bam

Any thoughts?

Thanks,

Ilya

*Ilya Chorny Ph.D.*

*Bioinformatics Scientist I*

*Illumina, Inc. *

9885 Towne Centre Drive

San Diego, CA 92121

Work: 858.202.4582

Email: icho...@illumina.com <mailto:icho...@illumina.com>

Website: www.illumina.com <http://www.illumina.com>



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