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: ichorny@illumina.com <mailto:ichorny@illumina.com>
Website: www.illumina.com <http://www.illumina.com>
___________________________________________________________ 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: