Bypass prescreen always = True

Microbial community profiling HUMAnN
1

i have installed humann 3.6.1 by pip install humann --no-binary :all: -i https://pypi.tuna.tsinghua.edu.cn/simple, but it always run by
RUN MODES

resume = False
verbose = False
bypass prescreen = True
bypass nucleotide index = True
bypass nucleotide search = False
bypass translated search = False
translated search = diamond
threads = 14

my code is humann --input /mnt/qc/MHBA/MHBA1/MHBA1.fastq --output /mnt/gongneng --threads 2 --metaphlan-options="--bowtie2db /mnt/shujuku/humann3/metaphlan --index v30_CHOCOPhlAn_201901" --bypass-nucleotide-index, and i have set bypass prescreen = False before run humann.

2

Hi, Thank you for the detailed post. If you set --bypass-nucleotide-index it will search for a custom nucleotide database and will set bypass prescreen to True.

Thank you,
Lauren