you didn't specify what clustering method u r using. Are u using drmaa or pbs? 
With Regards,
Ambarish Biswas,
University of Otago
Department of Biochemistry,
Dunedin, New Zealand,
Tel: +64(22)0855647
Fax: +64(0)3 479 7866

On Fri, Jul 29, 2011 at 10:03 AM, Shantanu Pavgi <pavgi@uab.edu> wrote:

We experienced an issue where some of the galaxy jobs were sitting in the 'new' state for a quite long time. They were not waiting for cluster resources to become available, but haven't been even queued up through DRMAA. We are currently using non-debug mode and following were my observations:
* No indication of new jobs in paster.log file
* database/pbs script didn't contain any associated job scripts
* in backend database - job table contained their galaxy job id but no command_line input was recorded

Also, not all the jobs are waiting in the 'new' state. Many jobs submitted after above waiting jobs got completed successfully on the cluster. Is there any job submission logic within galaxy which is being used for submitting jobs? Any clues on how to debug this issue will be really helpful.

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