Hi Ha,
More than likely, the problem is your rule file isn't sufficient for circuit extraction. You need to have circuit extraction rules in order for the netlist to get extracted properly. If necessary, you can include them using an INCLUDE statement in your rule header file.
layout.spi is simply the name of a SPICE file that 'calibre –spice' creates. I wanted to see if you could successfully extract a SPICE netlist. It sounds like the answer is no.
dan