Currently there is a problem which causes the rgoaat to crash with the message:
Aperture 2 not defined
The only way out of this (that I currently know of) is to type:
after each run of rgoaat
To remove the offending files that seem to hang around after the completion of the reduction routine. This is being looked at. Since the GUI version of the system doesn't allow you to do this, you should really run in the non-GUI version for the time being.