Hello Elwood,
The public Main Galaxy server was very busy this weekend this likely
contributed to the problems you were having with loaded and possibly
with job execution.
First, be sure that you are loading with FTP and confirming that loading
is successful with a client during this time. This also permits
interrupted loads can be restarted as necessary.
http://wiki.galaxyproject.org/FTPUpload
For the Tophat job, there were some known job failures related to load.
I would restart the job and see if a new run resolves the issue. If the
problem is persistent, please submit the new error as a bug report and
we can take a closer look. Be sure to leave all inputs and both Tophat
runs active (undeleted) if you submit a bug report, as a history is
often very helpful/necessary when diagnosing a problem.
Sorry that you were having problems, but hopefully these can be resolved
quickly.
Best,
Jen
Galaxy team
On 5/7/13 6:34 AM, Elwood Linney wrote:
Hello, I have successfully used the public server for processing
RNAseq data but I have run into some problems this weekend. And this
weekend there were various times when I would get a message that
Galaxy was not available.
Specifically, I received some new 50bp single-ended RNAseq data and
proceeded to process it through the public server as I have done
successfully before.
I concatenated it the subfiles into one fastq file, transferred it to
Galaxy, groomed it just to be safe, looked at its quality and did not
have to trim it and then I passed it on to Tophat. [all in the same
manner that had worked for me before]
It consisted of 4, approximately 15gb files. While i was moving these
files individuallly into the Tophat stage this weekend there were
interruptions in the availability of Galaxy. I waited during the
weekend, one set of the 4 Tophat files for one of the 4 datasets was
processed but then 1 file that I had processed during the interruption
turned out to have errors, so I deleted it and re-entered it, another
set was processing overnight and then it turned out to have errors.
So thinking that maybe 3 of the 4 sets for some reason had problems, I
deleted them, re entered them. One was going overnight and into the
day and this morning it had errors.
Since i am not sure how to read these errors, I am at a loss as to
what is happening, particularly since one of my files was successfully
processed through Tophat. This is the readout for one of the 4 Tophat
files that were in error. Any advice on this would be welcome since I
hope to soon have a 64gb ram computer with 12 cores to transfer Galaxy to.
43: Tophat for Illumina on data 8: accepted_hits
error
An error occurred with this dataset: /TopHat v1.4.0 tophat -p 8
/galaxy/data/danRer7/bowtie_index/danRer7
/galaxy/main_pool/pool7/files/006/143/dataset_6143636.dat Exception in
thread Thread-1: Traceback (most recent call last): File
"/usr/global/python/2.6.5/lib/python2.6/threading.py", l/
Sincerely,
Elwood Linney
Duke University Medical Center
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
