# Running OptiMAS in command line

For the three different operating systems you will need to specify a list of 6 mandatory arguments (1-6) (plus one optional argument, 7) to run optimas command line executable (for example):

$ optimas input.dat[1] input.map[2] 0.000001[3] 0.0[4] output_folder[5] 0[6] [verb][7]

[1] - Input file: path to the genotype/pedigree file (.dat).
[2] - Input file: path to the genetic map input file (.map).
[3] - Algorithm parameter: cut-off (float number, 0.000001 by default), genotypic probability below which a rare phased genotype (diplotype see definition below) is removed and no more considered in subsequent computations.
[4] - Algorithm parameter: cut-off (float number, 0.000000 by default) for gametic probability. It corresponds to the probability that the number of crossovers expected in the region between flanking markers exceeds a given value. Thus, unlikely gametes with number of crossovers over this value are removed and no more considered in subsequent computations. Use of this option with values up to 0.01 is recommended in case many flanking markers per QTL lead to high computation time with default option.
[5] - Output folder: path to the output folder where the results will be stored (see section 4.2 for output description) the name of this directory must be changed from one run to another.
[6] - Algorithm parameter: 0 (by default), all the QTL present in the input files will be analyzed. 1-n (integer number), if you want to run the computations for a specific QTL.
[7] - Algorithm option: verb (optional here but used by default in the GUI version) for verbose mode. Verbose mode creates two files per QTL position, reporting respectively gamete and diplotype probabilities for all individuals. WARNING: With large/complex data, both files may take a lot of disk space, it is then recommended to disable this option.