Do you mean that your perl script actually quits when system is called, and you never reach your "if" statement?

If the qsub you are referring to is the SGE submission command, then I can think of a couple of potential solutions. I do not have much experience with SGE, but when I google qsub, and search for "wait", I see the "-sync" option, which states: 

-sync y[es]|n[o]
    Available for qsub.

    -sync y causes qsub to wait for  the  job  to  complete
    before  exiting.   ...

[download]

Another possibility is to submit the job as you are doing, then wait for the job to finish by polling its status using qstat.

In reply to Re: submitting job to a queue by toolic
in thread submitting job to a queue by mjr1n1

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