You don't mention if your PEX is xRC or xACT (I assume not xL, as you only mentioned R and C) but there are several command-line examples given in the xRC/xACT product manuals. For PEX, you'll need a minimum of 3 invocations: the first to build the PHDB (with the right SVRF options, the LVS run can be used for this), the second to build the parasitics database (PDB), and the third to output the netlist(s). To specify the types of parasitics, you can either do a simple run where only those are extracted and then netlisted, or you can do something more complex with a fuller PDB and then outputting specific sets of parasitics. The product manuals are xrc_user and xact_user (no "calbr_" prefix), available in your documentation tree.
For PERC, most of the complexity is in the rules, so invocation is pretty simple. In the 2016.4 calbr_perc_user, the sections you want are "calibre -perc" (simple example and explanation of all the invocation options) and "Set Up and Run Calibre PERC" (more details on all the parts).
Incidentally, if you are already able to run using Calibre Interactive, you can convert your GUI-based runs into batch-executable scripts. See "Running Calibre Interactive in Batch Mode" for information on converting.
Hope this helps-
Thank you for the quick reply. I will try this out after going through the manual. I am new to this, so might need a little guidance from you .
Extraction mode is xRC