STRATIX II fpga is not getting initialized

We are trying to confugure stratix II fpga(EP2S90H484C4) in JTAG mode. The config done pin is going high but init_done pin is not going high. The init_done pin is enabled in quartusII software and a pullup is also connected to the init_done pin. The init done pin goes low once the configuration starts but it is never becoming high later. There is not output from the fpga. what could be the problem in this case. Have anybody faced such a problem.

Thanks in advance,

Suvedha