Sounds like you're instatiating SignalTap in Megawizard? That's possible, but surely not the usual way and simple to operate Signaltap, which is by opening SignalTap tool respectively creating a new SignalTap file and select clock and acquired signals. Trigger conditions for the basic trigger are simply selected from acquired signals in the GUI. Or are you working with Quartus linux version and don't have a SignalTap GUI? (I'm only guessing, never saw this tool at work)
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Acquistion in progress, Acquring pre-trigger data.
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means, that SignalTap is waiting for a trigger condition (which apparently isn't ever met).