On 06/28/2011 07:06 PM, colin molter wrote:
hi hans,
you are right.
it seems that even if i stopped galaxy
(i just stopped the run.sh command)

i still have a job running:
root     10441 97.0  0.0  77496  1772 pts/6    R    11:59 402:48 python
/opt/galaxy-central/tools/fastq/fastq_groomer.py /fs1/GenomicsData/ERP0005

it seems that the transformation of a fastq file is taking a lot of time (it
uses 100%of cpu since 7hours).
does it sound normal?

I am not very familiar with 'fastq_groomer.py' and without knowing the size of your fasta file, it is impossible to tell.

Have you tried a subset of your fasta file? May be your data is corrupt resulting in an endless loop?


i think i have better to kill that job and to try another way.

i stopped the job and it works

2011/6/28 Hans-Rudolf Hotz<h...@fmi.ch>

Hi Colin

  I launched a big job on my local galaxy server (for which I am admin). The
job was to put local dir in the datalist.
It took too long and i wanted to stop it .... but how?? i failed to find a

go to the admin view ->  'Manage jobs' and there you can kill individual

  To stop the job i thought that stopping the galaxy running instance could
make it. (AM I RIGHT?)

possible, but sounds like an 'overkill' to me. I would first try the 'soft'
method described above....and use this only as a last resort.

  Unfortunately, i failed to restart galaxy. I have the following error:

are you sure you have killed the galaxy process? Since this part of the
error message tells me that Galaxy (or another service) is still using the
port number.

socket.error: (98, 'Address already in use')

How did you stop galaxy?

Regards, Hans

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