Immcantation/Change-O package set is for VDJ assignment. Clonal assignment is done by Immcantation/SCOPer. The result for VDJ assignment is stored in the folder vdj_annotation. It's always there no matter how you set "skip_all_clones_report".

Hi, thank you for your replies. I will look into this after the weekend, i may return with additional questions 🙂

Sure. No problem.