Programming .sof file with nios dev kit stratix

Make sure that you have the Unused Pins for your Quartus project set to be Inputs Tristated. You can do this as follows after the project is opened in Quartus:

1. Click on Assign --> Device

2. Click on the Device and Pin Options Button

3. Click on the Unused Pins Tab.

4. This should be the first Radio button.

Just to elaborate on why this is:

A feature of the Nios development boards is to demonstrate remote

reconfiguration. This is done via an FPGA I/O which is connected to

the MAX CPLD on the board. The MAX CPLD is programmed to re-configure

the FPGA when the signal is driven low (in this way, the FPGA can send

a signal telling the MAX chip to reconfigure itself). For reference

designs that include this pin and leave it high, or tri-stated, there

is no issue. However, a user design must either drive this pin high

manually, tri-state the pin manually, or leave the pin un-assigned and

tri-state the unused outputs (as Subroto's instructions indicate).