SAMUEL Q&A

[Q] How to submit SAMUEL jobs on MSG cluster using QSUB?
[A] Many SAM scripts can use more than 1 CPU, such as samautopick.py, samfrealign.py, samrefine.py, samclasscas.py, etc.

  1. Set up the script the same way as for single computer, and specify how many CPUs to use.
  2. Create a new file (e.g. "run.sc") like following:
    #!/bin/csh
    #$ -pe cpu 8
    #$ -cwd
    #$ -j y
    #$ -S /bin/csh
    samautopick.py '-img_####.dat' autoref.dat 8 4,23 1-100
  3. Make it executable by "chmod +x run.sc".
  4. Submit the job by "qsub run.sc".