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I submit a job to SGE using the qsub command and get the error:

qsub: Unknown option

What unknown option?

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    perhaps giving the submission file would help diagnose the problem? – Bruce Becker Oct 23 '18 at 12:02
  • @BruceBecker, I answered this myself. The answer shows the offending line in the submission file. – John McGehee Oct 24 '18 at 17:55
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You can specify qsub command line options within the script on lines beginning with #$. For example:

#$ -S /bin/bash

If #$ is not followed by a valid qsub option:

#$ -invalid_qsub_option

You get the unhelpful message:

qsub: Unknown option

If you get this message, search the script you are submitting for #$ and make sure it is followed by a valid qsub command line option.

If you are really must keep your lines beginning with #$, you can specify a different prefix string using the qsub -C command line option.

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