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Using Cyclone V qsys eclipse hello world error

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I'm using the cylone V FPGA starter kit dev board. I have all my peripherals built in quartus/qsys and everything compiles just fine. Using the nios II system builder in eclipse I start the hello world program. Everything again compiles with no problem. i then program the FPGA in quartus with the .sof file. i then use the nios II programmer to try and install the .elf file. The programmer says it can not connect to the jtag. If i reset the FPGA it's able to connect to the jtag. Any reason why this is happening?
 

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