What exactly is the command line you are using? What file do you specify in the LAYOUT PATH in the SVRF file?
If you take a look at example 2 in "Calibre nmLVS and Calibre nmLVS-H Command Line" in the calbr_ver_user.pdf, you'll see you need to set the Layout Path to a SPICE file, not a GDS as well as setting Layout System to SPICE. (You may also find example 5 useful.)
Hi Samantha. I see now. I needed to edit the LAYOUT PATH and SYSTEM in the SVRF file so that it uses the .sp file instead of .gds.
There's one more way you might be interested in too... (if you're already using command line batch mode)
% calibre -lvs -hier -spice layout.spi
(using the actual name of the layout netlist you already have in place of layout.spi)
That -spice switch on the command line overrides the LAYOUT PATH and LAYOUT SYSTEM in the rule file in case you want to use the same exact rule file, with no changes, for separate connectivity extraction and LVS comparison jobs.