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An example of successful run command is presented below. Arguments in "<>" brackets are absolute paths to files.

cc.bin -n 16 -i <matrix_input_file> -o <clusters_out> -c <profiles_out> -p <CAG_prefix> --max_canopy_dist 0.1 --max_close_dist 0.4 --max_merge_dist 0.1 --min_step_dist 0.005 --max_num_canopy_walks 5 --stop_fraction 1 --canopy_size_stats_file <progress_stat_file>

To interrupt the process (on SUSE) and initiate output preparation (which may take hours)

kill -INT [ PID ]

... TODO