How to check clk and reset signal when ELF downloading failed?

I learnt from the forum that an ELF downloading failure is likely to be caused by an incorrectly set clk signal or reset signal. The problem is how I can check the clk or reset signal without running the nios program?

My design is a qsys project consisting of nios, some peripherals including external ddr-ram controller and a custom module connected through avalon-mm bus. The system works under a single clock domain generated by the pll that comes with the ddr-ram controller. Reset signal is connected to LOW directly.

Timing requirement was met with some unconstrained paths (input/output ports and paths) which should be fine because previously a similar system ran successfully with these paths unconstrained. Any suggestion will be appreciate.

Thanks guys.