Due to a problem in the Intel® Quartus® Prime software version 16.1 Update 2 and earlier, you may see the error message above in the fitter stage when your design has an External Memory Interface (EMIF) block tied to lower level of entity. The EMIF PLL reference clock cannot be detected if the design has a wrapper around it.
Intel Software: Quartus Prime Pro, Quartus Prime Standard
Last Modified: Sun Apr 07 2019 19:19:00 GMT-0700
Version Found: v16.1 Update 2
Version Fixed: v17.0
Bug ID: 2205972877