Thanks for the advice, after a little trial and error I managed to upload a firmware.
The issue I now have is timeouts when trying to program it.
if I try to upload blink with the web editor I get -
Upload started
Programming with: Serial
Flashing with command:/home/dave/.arduino-create/arduino/avrdude/6.3.0-arduino17/bin/avrdude -C/home/dave/.arduino-create/arduino/avrdude/6.3.0-arduino17/etc/avrdude.conf -v -patmega2560 -cwiring -P/dev/ttyACM0 -b115200 -D -Uflash:w:/tmp/arduino-create-agent918660697/Blink.hex:i
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 "/home/dave/.arduino-create/arduino/avrdude/6.3.0-arduino17/etc/avrdude.conf"
User configuration file is "/home/dave/.avrduderc"
Using Port : /dev/ttyACM0
Using Programmer : wiring
Overriding Baud Rate : 115200
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
avrdude done. Thank you
I'm not sure If I made a mistake and selected the wrong hex when updating the firmware.
I get the following now
$ lsusb
Bus 003 Device 005: ID 2341:0042 Arduino SA Mega 2560 R3 (CDC ACM)
$ dmesg
[ 5322.852900] usb 3-2: new full-speed USB device number 5 using xhci_hcd
[ 5323.035892] usb 3-2: New USB device found, idVendor=2341, idProduct=0042, bcdDevice= 0.01
[ 5323.035899] usb 3-2: New USB device strings: Mfr=1, Product=2, SerialNumber=220
[ 5323.035902] usb 3-2: Manufacturer: Arduino (www.arduino.cc)
[ 5323.035904] usb 3-2: SerialNumber: 85036313230351900231
[ 5323.082963] cdc_acm 3-2:1.0: ttyACM0: USB ACM device
$ usb-devices
T: Bus=03 Lev=01 Prnt=01 Port=01 Cnt=01 Dev#= 5 Spd=12 MxCh= 0
D: Ver= 1.10 Cls=02(commc) Sub=00 Prot=00 MxPS= 8 #Cfgs= 1
P: Vendor=2341 ProdID=0042 Rev=00.01
S: Manufacturer=Arduino (www.arduino.cc)
S: SerialNumber=85036313230351900231
C: #Ifs= 2 Cfg#= 1 Atr=c0 MxPwr=100mA
I: If#=0x0 Alt= 0 #EPs= 1 Cls=02(commc) Sub=02 Prot=01 Driver=cdc_acm
I: If#=0x1 Alt= 0 #EPs= 2 Cls=0a(data ) Sub=00 Prot=00 Driver=cdc_acm