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Sure you can. Every output in Studio One has metronome on/off and metronome level controls. Once you set up a cue mix for your monitor (or use main out for simple uses) go to that output and you'll find them.
cue metronome.png


NB. Ah, now I understand. You're recording the output from the synth which now also includes the metronome. Hmm, tricky. Does your synth have more than output to computer? How does it show up in the I/O settings? Can you set the send from the synth to before where synth sound and metronome are mixed?
 
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If your synth-also-interface can't send the synth audio output to Studio One before mixing in the Audio (to the speakers) then you have to do this in two passes: First record the midi (which metronome in output), then play the midi back to the synth and record the audio (without metronome).
 
....but when i’m recording the midi into audio
this is the problem how do i get it to record just the seqtrak instrument ?
Use the Studio One's metronome as shown. Its ultimately going to synchronize with your Yamaha seqtrak just the same, providing you dont encounter latency. You'll be monitoring the Yamaha as well through your headphones. Only the metronome won't end up as part of the recording.

Either that, or have you seqtrak (which I'm not familiar with), play the metronome on a different MIDI channel that you hear but dont record to. Based on however it outputs audio. The process here is pretty straight forward, but perhaps I'm missing some limitation to the seqtrak. In that case, monitor the metronome using Studio One.
 
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