Due to a problem in Intel® Quartus® Prime Pro/Standard Software, OSC_CLK_1_HPS, nPOR_RST and nRST_HPS input ports are disabled by U-boot settings.
1) Move to the hps_isw_handoff folder in your design.
2) Open hps.xml
3) Find the following section.
<csr>
<!-- Unused pin 1 -->
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.rtrim' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.input_buf_en' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.wk_pu_en' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.pu_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.pd_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.pu_drv_strg' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.pd_drv_strg' value='0' />
<!-- Unused pin 2 -->
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.rtrim' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.input_buf_en' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.wk_pu_en' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.pu_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.pd_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.pu_drv_strg' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.pd_drv_strg' value='0' />
<!-- Unused pin 3 -->
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.rtrim' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.input_buf_en' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.wk_pu_en' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.pu_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.pd_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.pu_drv_strg' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.pd_drv_strg' value='0' />
4) Replace above 3 unused settings with the following OSC_CLK_1_HPS, nPOR_HPS and nRST_HPS settings, and save hps.xml.
<csr>
<!-- OSC_CLK_1_HPS -->
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.rtrim' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.input_buf_en' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.wk_pu_en' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.pu_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.pd_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.pu_drv_strg' value='8' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_1.pd_drv_strg' value='10' />
<!-- nPOR_HPS -->
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.rtrim' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.input_buf_en' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.wk_pu_en' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.pu_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.pd_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.pu_drv_strg' value='8' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_2.pd_drv_strg' value='10' />
<!-- nRST_HPS -->
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.rtrim' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.input_buf_en' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.wk_pu_en' value='1' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.pu_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.pd_slw_rt' value='0' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.pu_drv_strg' value='8' />
<config name='i_io48_pin_mux_dedicated_io_grp.configuration_dedicated_io_3.pd_drv_strg' value='10' />
5) Create one uboot project and make the bin file based on new handoff file