There appears to be a typo in the lmm.cpp file for gemma 0.98.4 (and some older versions, but not sure how far back it goes). In the line defining infilen in LMM::AnalyzeBimbamGXE, auto infilen = file_gene.c_str(), I think this should be auto infilen = file_geno.c_str(), i.e. file_gene should be file_geno. Otherwise, there is a problem reading the bimbam input.
There appears to be a typo in the lmm.cpp file for gemma 0.98.4 (and some older versions, but not sure how far back it goes). In the line defining infilen in LMM::AnalyzeBimbamGXE,
auto infilen = file_gene.c_str(), I think this should beauto infilen = file_geno.c_str(), i.e. file_gene should be file_geno. Otherwise, there is a problem reading the bimbam input.