Due to a problem in the Quartus® Prime Pro Edition Software version 24.1, you may see a fitter error below when multiple different protocol IPs and two System PLL are implemented in a single GTS transceiver bank.
Critical Warning: Could not find XCVR clock for my_directphy_inst_1|my_directphy|g1.n.sys[0].n_channel_superset_ip_inst|n_channel_superset_top_wrapper|hal_top_wrapper_inst|hal_top_ip|one_lane_inst_0|one_lane_hal_top_p0|pldif_hal_top_inst|pldif_hal_top|pldif_hal_coreip_inst|gen_sm_ch4_pldif_inst.ch4_pldif_inst|x_std_sm_hssi_pld_chnl_dp_0|o_hio_user_tx_clk1_clk
Error (332000): ERROR: Argument <node_object> is an object filter that matches no objects. Specify one matches only one object.
There is no workaround for cases where both PCIe and non-PCIe protocols are used in the same transceiver bank and each requires a System PLL.
This problem is fixed beginning with the Quartus Prime Pro Edition software version 24.2.