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: [email protected] <mailto:[email protected]>
Website: www.illumina.com <http://www.illumina.com>
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