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SCALEIT prints a ton of output, and in my experience, it is usually not a source of errors. So, I propose that there could be two flags, --verbose and --verbose-scaleit; the --verbose flag prints information for phenix and python, but does not print out all of the SCALEIT output. The --verbose-scaleit flag could be used in case the SCALEIT output is required for debugging.
This could be more sophisticated and make phenix outputs optional as well, but in my experience, a lot of matchmaps debugging is phenix debugging, so I think that's a good default.
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