With simple, line based calculations like filtering, counting etc. you could become I/O-bound rather than CPU-bound. Assuming a similar TB size of the output file, much time is wasted by disk seeks. Just look at and hear the disk drive: Noisy sounds and flashing lights are clear indicators of seek problems.

Two seperate physical disks avoid that. For less than an hours salary your problems could be gone. But do your benchmarks first!