This a repetitive flight and using most default settings. It is running a lot slower in Step 2 than normal. The flight does have some dirty edges that aren’t normally as bad. Would not think that would create such a slow run time.
it is hard to tell what doesn’t work without more information. Could you please share the log file of your project? This will provide information on the ongoing processing, the hardware, the resolution of the images,…and should enable some more comments and suggestions.
What I can suggest in the meantime, is to try out the software Pix4Dmatic for your processing. The software is much faster and is built for larger datasets such as yours. You can try it out here: https://www.pix4d.com/download/pix4dmatic
What are the deliverables you need at the end of the processing? e.g. only the dense point cloud, or more.