How can I...

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How can I record my two audio interface inputs in independents mono channels?

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Normally, you can't. JACK only works on one single audio device interface or soundcard.
However, with extra effort, there's ways to make it work with additional devices, assuming you don't want to deal with pulseaudio: try using the alsa_in/alsa_out or zita_a2j/zita_j2a, so called ALSA-to-JACK bridges.

any of those are tools that lets you add an ALSA device as a regular new client to JACK; they account to adapt and resample the PCM signal as much as it possibly can, as long as is certain that different devices have different clocks and time-bases and will drift apart from each other; of course, best results are due on the best (and expensive) devices, but then, one should consider to use one single multi-input/output interface, if you're after pro-audio standards :)

cheers

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