Top and qstat are generic unix utilities for tracking jobs. Running 'man
command' will, assuming they are installed on your system, provide the best
information for using them.
J.
On Dec 29, 2011, at 12:09 PM, Bassam Tork wrote:
Dear Jeremy,
Thank You very much, I will try your suggestion. Could you please guide me to
the link/webpage that talks about checking the job manually using
top/qstat/similar.
Happy New Year,
Bassam Tork.
On Thu, Dec 29, 2011 at 9:18 AM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
My idea was to pass all above including main.bash as parameters to the
python wrapper (called run.py, attached), as follows:
where the last parameter sys.argv[7] is the output file, specified by xml
file.
This is the correct approach.
But galaxy was running for more than 3 hours, although it should take
only 7-10 minutes on our server with no results.
Vispa should write its output to dataset_192_I_2_20_CNTGS_DIST0_EM20.txt
, where dataset_192 .txt is the reads file.But
dataset_192_I_2_20_CNTGS_DIST0_EM20.txt did not appear in
galaxy-dist/database/files/000.
run.py: simply coppies data from dataset_192_I_2_20_CNTGS_DIST0_EM20.txt to
galaxy output file, but nothing is coppied since
dataset_192_I_2_20_CNTGS_DIST0_EM20.txt was not created.
How could the results appear?Could somebody help me ?
The first thing to check is if run.py functions correctly outside of Galaxy.
If so, try checking the job manually using top/qstat/similar system utilities
to figure out where the job is stuck.
Good luck,
J.
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