[galaxy-user] 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

[Jennifer 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

Post by 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