Hello,
I'm using Nebula and when I try to use the annotation tools (genomic
annotation and gene annotation in NGS annotation menu) I got always this
error despite of the bed file that I use:
An error occurred running this job:Unable to run this job due to a cluster
error
Could you indicate me how to solve this?
Regards,
Gema
From: Jennifer Jackson <j...@bx.psu.edu>
Date: Wednesday, May 8, 2013 5:36 AM
To: Elwood Linney <ellin...@gmail.com>
Cc: <galaxy-u...@bx.psu.edu>
Subject: Re: [galaxy-user] problems with Tophat
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
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>
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>
> To manage your subscriptions to this and other Galaxy lists,
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>
> http://lists.bx.psu.edu/
>
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>
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>
--
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/
___________________________________________________________
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/
