If the average read length is very similar to your reference length then nanosim goes into an endless loop while trying to get a read to simulate about nanosim

[JustinChu]

Sorry for the late reply,

This can be prevented by using the --max_len option, set to your amplicon size. However, this is more of a hack, and ideally, you would simulate by training it first on a sequencing experiment with similar properties (sequencing of another library made using fragments of a similar size to the one being simulated).