Change the INPUT_TERMINATION of pin <pcie_refclk_name> to \'Transceiver Dedicated Refclk Pin Termination\' and select the appropriate Quartus® Settings File(QSF) assignments.
Refer to the Altera Transceiver PHY IP Core User Guide for more information on how to use these assignments.
As an example, the .qsf file will appears as below if the option DC_COUPLING_INTERNAL_100_OHM is used:
set_instance_assignment -name XCVR_REFCLK_PIN_TERMINATION DC_COUPLING_EXTERNAL_100_OHMS -to <pcie_refclk_name>