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 *
Hi, Try using the fastQ Groomer tool instead,, Grooming actually does take a while. There is also a faster parallel version of fastQ groomer on the main tool shed which you can try as well. Cheers, Kevin. On Thu, Oct 4, 2012 at 2:49 AM, Pete Schmitt <Peter.Schmitt@dartmouth.edu>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.eduhttp://columbia.dartmouth.edu/gridhttp://www.e...
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On Wednesday, October 3, 2012, 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.
That's strange - this should be really fast as it doesn't change the file on disk, just the metadata in Galaxy's database. (The FASTQ groomer is much slower because it does write a new file) Which Galaxy installation was this on? If yours, do you know anything about the setup (e.g. database used)? Peter
The installation is mine. It's using MySQL for the db. I have two other installations. This is the only one that holds the galaxy database directory on an nfs mount. The other two installations don't exhibit this problem. All 3 installations run on centos 5.8 using python 2.6. Sent from my iPad On Oct 5, 2012, at 3:24, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com>> wrote:
On Wednesday, October 3, 2012, 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.
That's strange - this should be really fast as it doesn't change the file on disk, just the metadata in Galaxy's database.
(The FASTQ groomer is much slower because it does write a new file)
Which Galaxy installation was this on? If yours, do you know anything about the setup (e.g. database used)?
Peter
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
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participants (4)
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Andreas Kuntzagk -
Kevin Y -
Pete Schmitt -
Peter Cock