Due to a problem in the Quartus® II software version 12.1, this error may be seen when Level 4 debug is enabled within Nios II IP.
To workaround this issue in the Quartus II software version 12.1 follow the steps below:
1. Open the top level Qsys HDL file in a text editor
2. Change the port name "jtag_debug_clkx2" to "clkx2"
3. Recompile the design in Quartus II
Note: If you regenerate your QSYS system you will need to repeat the steps above.
This problem is scheduled to be fixed in a future release of the Quartus II software.