Due to an issue with the Quartus® II software version 12.0 and later, this error may occur the Quartus II software output files is set to a directory other than the default location. The default location is the same location as the project.
To work around this problem, copy the generated .jdi file from the project output directory to the directory where the .qpf file is located. Open the External Memory Interface Toolkit and follow the normal procedure for connecting your design.
This issue has been fixed beginning with the Quartus II software version 12.1.