k options ignored - Githubissues

I am trying to run an assembly with only larger kmers, but the MEGAHIT appears to use the default kmer list. Is there something that I am missing? Code and options.json shown below. Thanks!

Code:

megahit -1 trimmed_seqs_73/73_forward_paired.fq.gz,trimmed_seqs_74/74_forward_paired.fq.gz,trimmed_seqs_47/47_forward_paired.fq.gz,trimmed_seqs_48/48_forward_paired.fq.gz,trimmed_seqs_49/49_forward_paired.fq.gz,trimmed_seqs_50/50_forward_paired.fq.gz,trimmed_seqs_51/51_forward_paired.fq.gz,trimmed_seqs_52/52_forward_paired.fq.gz,trimmed_seqs_53/53_forward_paired.fq.gz,trimmed_seqs_54/54_forward_paired.fq.gz,trimmed_seqs_55/55_forward_paired.fq.gz \
    -2 trimmed_seqs_73/73_reverse_paired.fq.gz,trimmed_seqs_74/74_reverse_paired.fq.gz,trimmed_seqs_47/47_reverse_paired.fq.gz,trimmed_seqs_48/48_reverse_paired.fq.gz,trimmed_seqs_49/49_reverse_paired.fq.gz,trimmed_seqs_50/50_reverse_paired.fq.gz,trimmed_seqs_51/51_reverse_paired.fq.gz,trimmed_seqs_52/52_reverse_paired.fq.gz,trimmed_seqs_53/53_reverse_paired.fq.gz,trimmed_seqs_54/54_reverse_paired.fq.gz,trimmed_seqs_55/55_reverse_paired.fq.gz \
    --presets meta-large \
    -m 0.75 \
    --min-contig-len 500 \
    --k-list 67,75,83,91,99,107,115,123,131 \
    -o June_2018_assembly5\
    -t 32

options.json shows:

{"out_dir": "/home/8nd/BC_Virus_Rhizo/June_2018_assembly5", "temp_dir": "/home/8nd/BC_Virus_Rhizo/June_2018_assembly5/tmp", "test_mode": false, "continue_mode": false, "force_overwrite": false, "memory": 0.75, "min_contig_len": 500, "k_min": 27, "k_max": 127, "k_step": 10, "k_list": [27, 37, 47, 57, 67, 77, 87, 97, 107, 117, 127], "auto_k": true, "set_list_by_min_max_step": true, "min_count": 1, "has_popcnt": true, "hw_accel": true, "max_tip_len": -1, "no_mercy": true, "no_local": false, "bubble_level": 2, "merge_len": 20, "merge_similar": 0.95, "prune_level": 2, "prune_depth": 2, "num_cpu_threads": 32, "disconnect_ratio": 0.1, "low_local_ratio": 0.2, "cleaning_rounds": 5, "keep_tmp_files": false, "mem_flag": 1, "out_prefix": "", "kmin_1pass": true, "pe1": ["/home/8nd/BC_Virus_Rhizo/trimmed_seqs_73/73_forward_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_74/74_forward_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_47/47_forward_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_48/48_forward_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_49/49_forward_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_50/50_forward_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_51/51_forward_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_52/52_forward_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_53/53_forward_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_54/54_forward_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_55/55_forward_paired.fq.gz"], "pe2": ["/home/8nd/BC_Virus_Rhizo/trimmed_seqs_73/73_reverse_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_74/74_reverse_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_47/47_reverse_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_48/48_reverse_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_49/49_reverse_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_50/50_reverse_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_51/51_reverse_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_52/52_reverse_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_53/53_reverse_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_54/54_reverse_paired.fq.gz", "/home/8nd/BC_Virus_Rhizo/trimmed_seqs_55/55_reverse_paired.fq.gz"], "pe12": [], "se": [], "presets": "meta-large", "verbose": false}

voutcn / megahit

k options ignored #313