Q: Why is it then when I submit a job I get the following warning: 

Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.

A: Your default shell is csh or tcsh. Both of those shells have limited support for a feature called "job control" found in bash or sh. Torque uses your default shell to run jobs so you'll see this warning. You can get around this warning by adding #PBS -S /bin/sh to your submit script. This tells Torque to launch your job using sh as the shell. This warning and workaround will not change the output of your job.