Nios tool error

Check that the CPU receives a clock, that its reset signal is not active all the time, and that you don't have a custom component that freezes the Avalon bus. You can use signaltap probes to check all that.

Check also that you have the license for the Nios processor. I had this problem recently: we have a single floating license for the Nios, but we are several working on different projects at the same time. When I compile the design, if the Nios license is already in use during the synthesis phase, Quartus doesn't stop. It just puts a warning saying it couldn't get a license for Nios, and continues compiling everything, with a disabled CPU. It took me a long time to understand what was happening...