Slight issue programming bootloader onto DIY Micro ATmega32u4

Using Arduino Programming Questions
1

Just made my own custom Arduino Micro to include couple extra buttons and a micro SD card reader, trying to use my Arduino Mega as ISP and burn the bootloader onto board; however I'm getting the following error message:

Arduino: 1.8.12 (Windows 10), Board: "Arduino Micro"

B:\Program Files (x86)\Arduino\hardware\tools\avr/bin/avrdude -CB:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega32u4 -cstk500v1 -PCOM3 -b19200 -e -Ulock:w:0x3F:m -Uefuse:w:0xcb:m -Uhfuse:w:0xd8:m -Ulfuse:w:0xff:m

avrdude: Version 6.3-20190619
Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
Copyright (c) 2007-2014 Joerg Wunsch

System wide configuration file is "B:\Program Files (x86)\Arduino\hardware\tools\avr/etc/avrdude.conf"

Using Port : COM3
Using Programmer : stk500v1
Overriding Baud Rate : 19200
AVR Part : ATmega32U4
Chip Erase delay : 9000 us
PAGEL : PD7
BS2 : PA0
RESET disposition : dedicated
RETRY pulse : SCK
serial program mode : yes
parallel program mode : yes
Timeout : 200
StabDelay : 100
CmdexeDelay : 25
SyncLoops : 32
ByteDelay : 0
PollIndex : 3
PollValue : 0x53
Memory Detail :

Block Poll Page Polled
Memory Type Mode Delay Size Indx Paged Size Size #Pages MinW MaxW ReadBack

eeprom 65 20 4 0 no 1024 4 0 9000 9000 0x00 0x00
flash 65 6 128 0 yes 32768 128 256 4500 4500 0x00 0x00
lfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
hfuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
efuse 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
lock 0 0 0 0 no 1 0 0 9000 9000 0x00 0x00
calibration 0 0 0 0 no 1 0 0 0 0 0x00 0x00
signature 0 0 0 0 no 3 0 0 0 0 0x00 0x00

Programmer Type : STK500
Description : Atmel STK500 Version 1.x firmware
Hardware Version: 2
Firmware Version: 1.18
Topcard : Unknown
Vtarget : 0.0 V
Varef : 0.0 V
Oscillator : Off
SCK period : 0.1 us

avrdude: AVR device initialized and ready to accept instructions

Reading | ################################################## | 100% 0.02s

avrdude: Device signature = 0xffffff (probably .avr8x_mega) (retrying)

Reading | ################################################## | 100% 0.02s

avrdude: Device signature = 0xffffff (probably .avr8x_mega) (retrying)

Error while burning bootloader.
Reading | ################################################## | 100% 0.02s

avrdude: Device signature = 0xffffff (probably .avr8x_mega)
avrdude: Yikes! Invalid device signature.
Double check connections and try again, or use -F to override
this check.

avrdude done. Thank you.

And was wondering what is going wrong, I have all the connections wired up correctly minus the power.

This was due to me realising I had connected the VCC on the ISCP header to 3.3V instead of 5V on my schematic; however this was sorted by simply connecting VCC to 3.3V on the mega instead of 5V.

2 
avrdude: Device signature = 0xffffff

That usually means a bad connection or the processor clock on the target processor is not running. Are you sure the ICSP header on your custom board is connected to all the right pins?

3

Please show us a wiring diagram and board schematics instead of a verbal description.

4

aarg:
Please show us a wiring diagram and board schematics instead of a verbal description.

Sure thing schematic is here:

1251×825 103 KB

Wiring from Mega to the ISCP header on the pcb board is as follows:

GND - GND
MOSI - Pin 51 (Mega)
VCC - 3.3V
MISO - Pin 10 (Mega)
SCK - Pin 51 (Mega)
RST - Pin 50 (Mega)

5 
MOSI - Pin 51 (Mega)
VCC - 3.3V
MISO - Pin 10 (Mega)
SCK - Pin 51 (Mega)
RST - Pin 50 (Mega)

That's the problem. The correct pins on the MEGA are:

MOSI -> Pin 51 (MOSI on the Mega)
MISO -> Pin 50 (MISO on the Mega)
SCK -> Pin 52 (SCK on the Mega)
RST -> Pin 10 (although SS defauts to 53 on the Mega)
6

Ah perfect, was just a case of switching the RST & MISO pin (the SCK pin 51 was a mistype as can't have sck & mosi on 1 pin).

Loaded bootloader and blink test works perfectly fine. Now I'm all set.