./runpath.sh ../data/2_ref.k55.simple.gml 3 0.01 ../data/2_ref.k55.simple.repeats 2_repeat.map ./runnode.sh ../data/2_ref.k55.simple.gml 3 1000 ../data/2_ref.k55.simple.repeats 2_repeat.map For both scripts: order is: [gml][cutoff][epsilon/nodes][repeat_file][map_file]