Hi,
I have a similar problem with renaming fastq to fastqsanger. In my case after
some time galaxy displays
"An error occurred setting the metadata for this dataset. You may be able to set it manually or
retry auto-detection."
The paster.log shows this:
galaxy.jobs DEBUG 2012-10-17 14:16:44,623 (123) Changing ownership of working directory with:
/usr/bin/sudo -E scripts/external_chown_script.py
/data/galaxy/galaxy-dist/database/job_working_directory/000/123 galaxy 3400
galaxy.jobs DEBUG 2012-10-17 14:16:44,989 Tool did not define exit code or stdio handling; checking
stderr for success
141.80.188.178 - - [17/Oct/2012:14:16:45 +0200] "POST /galaxy/root/history_item_updates HTTP/1.1"
200 - "http://bbc.mdc-berlin.de/galaxy/history?dataset_id=f30a35c999095ed7&filename=None";
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:16.0) Gecko/20100101 Firefox/16.0"
galaxy.datatypes.metadata DEBUG 2012-10-17 14:16:45,234 setting metadata externally failed for
HistoryDatasetAssociation 110: External set_meta() not called
galaxy.jobs DEBUG 2012-10-17 14:16:45,375 job 123 ended
May that be related to an incorrect setup of drmaa job-runner?
regards, Andreas
On 03.10.2012 18:49, Pete Schmitt wrote:
When attempting the change the filetype of a fastq file to fastqsanger, the
process for changing the
type goes on forever. This
does not allow any further processing of the data.
--
*
Pete Schmitt
Technical Director:
Discovery Cluster
NH INBRE Grid
Computational Genetics Lab
Dartmouth College, HB 6223
L24 Berry/Baker Library
Hanover, NH 03755
Phone: 603-646-8109
http://discovery.dartmouth.edu
http://columbia.dartmouth.edu/grid
http://www.epistasis.org
*
This body part will be downloaded on demand.
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany
http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
___________________________________________________________
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:
http://lists.bx.psu.edu/
