The Landsat calibration tool is expected the data as it is distributed from the USGS, which for a while now has been GeoTIFF with metadata (_mtl.txt). So the expected number of bands would be 4 for MSS and 6 for TM and ETM multispectral. Some older NLAPS data may include the thermal band within the MS bands if they were resampled but the file would still be in NLAPS format. If you have some other product, or the data is not in its original format as distributed from the data provider, then you won't be able to calibrate the data using this tool. If in doubt, you can always download Landsat data for free from the USGS.
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