slow running

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slow running

Emmanuelle Lerat
Hi everyone,

I am currently running a fastqgroomer on some data (about 7Go big). I am
surprise because I launched the analysis several hours ago and it is
still running. I am wondering if everything is alright since usually it
is faster than that, even on bigger dataset. I had the same problem
yesterday with fastQC that was not finished after 24h also it was
indicated as running (I finally discarded this job)

Is the galaxy sever busy or do you think it is because of my data?

thank you in advance for your help

Sincerely

Emmanuelle Lerat

--
Dr. Emmanuelle LERAT, CR1 CNRS, HDR

Laboratoire Biometrie et Biologie Evolutive
Universite Claude Bernard - Lyon 1
UMR-CNRS 5558 - Bat. Mendel
43 bd du 11 novembre 1918
69622 Villeurbanne cedex
France

Phone: 33+ 4.72.43.29.18
Fax:   33+ 4.72.43.13.88

http://lbbe.univ-lyon1.fr/-Lerat-Emmanuelle-.html

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Re: slow running

Jen Hillman-Jackson
Hi Emmanuelle,

I just went in and looked at your data. It appears that you uploaded a tar archive. That compression format is not supported. To load using FTP, these are the instructions. The "Upload" tool at the top of the tool panel can also be used and the usage is very similar. FTP is a two step process. FTP the file using a client, then load into your history using either tool (Get Data: Upload File, or Upload):
https://wiki.galaxyproject.org/FTPUpload

That said, sometimes with tar archives, the first file in the archive will be extracted and loaded. From a quick look this seems to be what resulted, but a closer look shows a few problems with the file extracted.

1. The file is truncated. I use the tool " Text Manipulation -> Select last lines from a dataset" to view the end of the file to see this.

2. The datatype ".fastqillumina" may or may not be the correct designator for the starting quality scores. Once you upload the file again (just the 'fastq" file, not the tar archive), run the tool "FastQC" to determine the correct dataytpe.

3. After that, then you can run the groomer as needed. The current groomer run you have going had setting that were a mismatch for the input datatype that you had set. This wiki explains how to do all of this correctly:
https://wiki.galaxyproject.org/Support#Dataset_special_cases

As you go through this, please leave datasets undeleted in case you would like feedback. I wasn't able to look at all of the steps you did since some were permanently deleted. Then once confirmed as OK, you can delete/perm delete what isn't needed.

When you step the current jobs, you can delete, then perm delete all data to completely stop the processes (and all associated data) to recover disk space.

Hopefully this helps things go smoother this time,

Jen
Galaxy team

On 5/27/14 3:58 AM, Emmanuelle Lerat wrote:
Hi everyone,

I am currently running a fastqgroomer on some data (about 7Go big). I am surprise because I launched the analysis several hours ago and it is still running. I am wondering if everything is alright since usually it is faster than that, even on bigger dataset. I had the same problem yesterday with fastQC that was not finished after 24h also it was indicated as running (I finally discarded this job)

Is the galaxy sever busy or do you think it is because of my data?

thank you in advance for your help

Sincerely

Emmanuelle Lerat


-- 
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

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
http://galaxyproject.org
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