From your message, I’m guessing that it occurs due to inconsistent setting with ‘vcv_matrix’ and ‘analysis_atom’ in [OPTION], and ‘fitting_atom’ in [FITTING].
Both ‘analysis_atom’ and ‘fitting_atom’ are required even though you don’t need to fitting or the two groups are same.
Please read the following instruction and check your input. https://www.r-ccs.riken.jp/labs/cbrt/samples/flccrd_analysis/