usage: kneaddata [-h] [--version] [-v] -i INPUT -o OUTPUT_DIR
[-db REFERENCE_DB] [--bypass-trim]
[--output-prefix OUTPUT_PREFIX] [-t <1>] [-p <1>]
[-q {phred33,phred64}] [--run-bmtagger] [--run-trf]
[--run-fastqc-start] [--run-fastqc-end] [--store-temp-output]
[--remove-intermediate-output] [--cat-final-output]
[--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--log LOG]
[--trimmomatic TRIMMOMATIC_PATH] [--max-memory MAX_MEMORY]
[--trimmomatic-options TRIMMOMATIC_OPTIONS]
[--bowtie2 BOWTIE2_PATH] [--bowtie2-options BOWTIE2_OPTIONS]
[--no-discordant] [--cat-pairs] [--reorder] [--serial]
[--bmtagger BMTAGGER_PATH] [--trf TRF_PATH] [--match MATCH]
[--mismatch MISMATCH] [--delta DELTA] [--pm PM] [--pi PI]
[--minscore MINSCORE] [--maxperiod MAXPERIOD]
[--fastqc FASTQC_PATH]