Hi,
I think there is a small issue in the implementation in AT of the new BoostedToptTagging: https://its.cern.ch/jira/browse/ANALYSISTO-793
When running with the systematic uncertainties the branches that contain the vector with jet tagger information get repeated multiple times in the nominal and systematic trees. The reason, I think, is that the vector that contains the names of the branches get incremented for each systematic and never cleaned in the EventSaver, cleaning it in the loop should solve the situation.
I opened also a ticket describing the problem:https://its.cern.ch/jira/browse/ANALYSISTO-810
Cheers Federica