Hi Lesa,
I have not been able to reproduce your error. For me, GGIR runs smoothly and generates all the expected reports.
The error indicates that something goes wrong with matching the milestone files from the various GGIR parts. To address this you may want to start with a new output folder. Also deleting the config.csv file in the output folder may help as GGIR tries to use that to load previously used function arguments.
I am using the latest GGIR development version, but would be surprised if that explains the difference.
Good luck,
Vincent
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