Trouble flashing hex file using avrdude

[OverripeBanana]

I've been trying to flash my Arduino Uno R3 with a hex file (it has hoodloader2 installed). I used the command recommended in the wiki.

Something like this:
avrdude.exe -C avrdude.conf -p atmega16u2 -c avr109 -b 1200 -P COM1 -U flash:w:Firmware.hex

Unfortunately, no matter what I try, I get this error:

avrdude error: programmer is not responding
avrdude error: programmer is not responding
avrdude error: programmer is not responding
avrdude error: programmer is not responding
avrdude error: programmer is not responding
avrdude error: programmer is not responding
avrdude error: programmer is not responding
avrdude error: programmer is not responding
avrdude error: initialization failed, rc=-1
- double check the connections and try again
- use -B to set lower ISP clock frequency, e.g. -B 125kHz
- use -F to override this check

avrdude error: programmer is not responding
avrdude error: programmer did not respond to command: leave prog mode
avrdude error: programmer is not responding
avrdude error: programmer did not respond to command: exit bootloader

avrdude done. Thank you.

I followed the recommendations given in the error message with no luck. Any help? I've been trying to fix this for hours, any help would be greatly appreciated. Thanks!