also I recommend that you change the behavior of --mode=contig/reads/both to: --only-output=contigs and --only-output=reads (also --mode=both should become the default behavior when user runs Falcon2Fastg, this does not need to be a command line parameter)
also I recommend that you change the behavior of --mode=contig/reads/both to: --only-output=contigs and --only-output=reads (also --mode=both should become the default behavior when user runs Falcon2Fastg, this does not need to be a command line parameter)