I have a huge confusion on whether or not this MCU(ATSAM4s4AA-AU) is supported by the ATMEL ICE debugger.
First, I checked the official website for ATSAM4S4A and when I got to the "Emulators and Debuggers" section, only the J32 Debug probe was shown.
Then I checked the IDE section and only Atmel Studio was shown as recommended IDE which is paradoxical since J32 debug port only works with MPLAB according to this document.
Then I checked an existing project that used Atmel ICE as a debugger using ATSAM4S16BA-AU-ND
This leads me to an assumption that ATMEL ICE would probably work since its documentation says that it works with "all SAM ARM Cortex-M based MCUs on both SWD and JTAG interfaces". However, I am still not 100% sure since I would not expect Microchip to make a mistake excluding ATMEL ICE from the official website link on ATSAM4S4.