cd hist_preparation/MC/fine_eta_bin/ or different subdirectory, i.e. hist_preparation/data/fine_eta_bin/ make ./Analysis___.x

cd JER/fine_eta_binning/ root -l gROOT->SetBatch(true) if you produce a lot of pdfs and a lot of canvas, without it, it will take ages to run .L iterFit.C++ compile the code mainRun(false,"/afs/desy.de/user/n/niedziem/public/histograms_mc_incl_full_fine.root","/afs/desy.de/user/n/niedziem/public/histograms_data_incl_full.root") path to root files you produced in histogram preparation part