If you are having trouble using the programmer on the VM, these solutions might help you a bit...

Run Quartus as root

1. Close out of any open instances of Quartus

2. Open up the terminal in the VM

3. Runsu to switch your terminal to root. The password is 341

4. Run /home/ece341/intelFPGA_lite/18.0/quartus/bin/quartus

5. Launch Quartus and attempt to program your board

Restart the jtag server

Sometimes, the jtag server will hang and become irresponsive. (If running the command that lists the jtag devices hangs, then this is your problem)

Nevertheless, running sudo killall -9 jtagd should fix this

Note: You theoretically shouldn't need to exit Quartus to do this