The first phase generates all of your proofs of space by creating seven tables of cryptographic hashes and saving them to your temporary directory. Phase 2 back-propagates through the hashes, phase 3 sorts and algorithmically compress these hashes in the temporary directory while starting to build the final file and phase 4 completes the file and moves it into your final plot file.
One of the major bottlenecks is usually the total sustained write speed of the disk underneath your temporary directory.