I suspect it simply runs out of memory, primarily because the automatic setting for repetitions for the DynamicalMatrix returns 5x5x3, and you end up with each calculation for the displacements having 5*5*3*12=900 atoms.
For a 2D material you only need 1 repetition in the C direction, but your system has a slightly too small vacuum spacing in the Z axis. So you can either increase this vacuum to 20 Å or so (and check in the Scripter or log file that it now correctly detects 5x5x1 repetitions), or just set the repetitions explicitly to 5x5x1 instead (300 atoms, big difference!).
