I am trying to program a Stratix V GX FPGA using Quartus Prime, but whenever I get to the Programmer window and select auto detect I get an error "Unable to scan device chain. On-board programming hardware is disabled." My board is powered, ON, and connected to my laptop via a Micro USB to USB A cable. I was following a tutorial https://software.intel.com/en-us/articles/how-to-program-your-first-fpga-device that teaches how to program with Quartus, it uses a different board as an example so I have tried to make it work for mine but I have issues when it comes to running the programmer, I instantly get a failed status. Any ideas?
Can you actually see your Stratix V device on the JTAG chain? If not, you have misconfigured your project. Another possibility is that indeed the on-board JTAG is disabled. This can happen when the board configurations pins are configured to use some pre-built image loaded via flash memory or even board DDR RAM. Double-check the board manual to check if there are DIP switches that control the configuration mode.