During tide-search, there is a progress indicator that shows how far the search has gotten. The progress indicator when p-values are turned off is
INFO: 1000 spectra searched, 7% complete
The progress indicator when it is turned on looks like this:
scan 1777 m/z 350.600000 charge 1 neutral mass 349.592724
The exact-p-value progress indicator should be modified to match the one used in a normal tide search. It should also use the "carp" facility so that progress gets stored to the log file.
I could swear I fixed that a couple of months ago. I'll check, but could you also confirm you are working with the current trunk?
I apologize. I forgot that my script was accessing an old version of the crux binary. I will resolve this issue.