After running the pin_assignments.tcl and performing compilation, you will get a warning as below:
Warning (181009): DQ I/O pins fed by DQS I/O pin "I/O pad mem_dqs[*]" assigned different I/O standards -- it is recommended that all DQ I/O pins fed by the same DQS I/O pin have the same I/O standard
This is because legality checks don't understand that differential and single-ended I/O standards are the same.
This issue has been fixed in Intel® Quartus® Prime Software version 13.0.