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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