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ATSAM3U2 Flash Controller needs to be initialized?

I designed a prototype using nRF52832 controller. On this prototype I was using the same Flash Controller ATSAM3U2 used on the nRF52DK.

I am bringing up the prototype and I was having problems with the ATSAM3U2 itself. 'nRF Go Studio' doesn't see the prototype, therefore I couldn't load any boot loader and could not program the on-board nRF52832.

I wonder how do I make a blank ATSAM3U2 from factory become similar to the ATSAM3U2 used on the nRF52DK? 

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