usage: humann [-h] -i <input.fastq> -o <output> [--threads <1>] [--version]
              [-r] [--bypass-nucleotide-index] [--bypass-nucleotide-search]
              [--bypass-prescreen] [--bypass-translated-search]
              [--taxonomic-profile <taxonomic_profile.tsv>]
              [--memory-use {minimum,maximum}]
              [--input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom}]
              [--search-mode {uniref50,uniref90}] [-v]
              [--metaphlan <metaphlan>]
              [--metaphlan-options <metaphlan_options>]
              [--prescreen-threshold <0.01>] [--bowtie2 <bowtie2>]
              [--bowtie-options <bowtie_options>]
              [--nucleotide-database <nucleotide_database>]
              [--nucleotide-identity-threshold <0.0>]
              [--nucleotide-query-coverage-threshold <90.0>]
              [--nucleotide-subject-coverage-threshold <50.0>]
              [--diamond <diamond>] [--diamond-options <diamond_options>]
              [--evalue <1.0>] [--protein-database <protein_database>]
              [--rapsearch <rapsearch>]
              [--translated-alignment {usearch,rapsearch,diamond}]
              [--translated-identity-threshold <Automatically: 50.0 or 80.0, Custom: 0.0-100.0>]
              [--translated-query-coverage-threshold <90.0>]
              [--translated-subject-coverage-threshold <50.0>]
              [--usearch <usearch>] [--gap-fill {on,off}] [--minpath {on,off}]
              [--pathways {metacyc,unipathway}]
              [--pathways-database <pathways_database.tsv>] [--xipe {on,off}]
              [--annotation-gene-index <3>] [--id-mapping <id_mapping.tsv>]
              [--remove-temp-output]
              [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
              [--o-log <sample.log>] [--output-basename <sample_name>]
              [--output-format {tsv,biom}] [--output-max-decimals <10>]
              [--remove-column-description-output]
              [--remove-stratified-output]

HUMAnN : HMP Unified Metabolic Analysis Network 3

optional arguments:
  -h, --help            show this help message and exit

[0] Common settings:
  -i <input.fastq>, --input <input.fastq>
                        input file of type {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom} 
                        [REQUIRED]
  -o <output>, --output <output>
                        directory to write output files
                        [REQUIRED]
  --threads <1>         number of threads/processes
                        [DEFAULT: 1]
  --version             show program's version number and exit

[1] Workflow refinement:
  -r, --resume          bypass commands if the output files exist
  --bypass-nucleotide-index
                        bypass the nucleotide index step and run on the indexed ChocoPhlAn database
  --bypass-nucleotide-search
                        bypass the nucleotide search steps
  --bypass-prescreen    bypass the prescreen step and run on the full ChocoPhlAn database
  --bypass-translated-search
                        bypass the translated search step
  --taxonomic-profile <taxonomic_profile.tsv>
                        a taxonomic profile (the output file created by metaphlan)
                        [DEFAULT: file will be created]
  --memory-use {minimum,maximum}
                        the amount of memory to use
                        [DEFAULT: minimum]
  --input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom}
                        the format of the input file
                        [DEFAULT: format identified by software]
  --search-mode {uniref50,uniref90}
                        search for uniref50 or uniref90 gene families
                        [DEFAULT: based on translated database selected]
  -v, --verbose         additional output is printed

[2] Configure tier 1: prescreen:
  --metaphlan <metaphlan>
                        directory containing the MetaPhlAn software
                        [DEFAULT: $PATH]
  --metaphlan-options <metaphlan_options>
                        options to be provided to the MetaPhlAn software
                        [DEFAULT: "-t rel_ab"]
  --prescreen-threshold <0.01>
                        minimum percentage of reads matching a species
                        [DEFAULT: 0.01]

[3] Configure tier 2: nucleotide search:
  --bowtie2 <bowtie2>   directory containing the bowtie2 executable
                        [DEFAULT: $PATH]
  --bowtie-options <bowtie_options>
                        options to be provided to the bowtie software
                        [DEFAULT: "--very-sensitive"]
  --nucleotide-database <nucleotide_database>
                        directory containing the nucleotide database
                        [DEFAULT: /share/biocore/projects/Internal_Jessie_UCD/Workshops/Metagenomics_and_Metatranscriptomics/References/databases/chocophlan]
  --nucleotide-identity-threshold <0.0>
                        identity threshold for nuclotide alignments
                        [DEFAULT: 0.0]
  --nucleotide-query-coverage-threshold <90.0>
                        query coverage threshold for nucleotide alignments
                        [DEFAULT: 90.0]
  --nucleotide-subject-coverage-threshold <50.0>
                        subject coverage threshold for nucleotide alignments
                        [DEFAULT: 50.0]

[3] Configure tier 2: translated search:
  --diamond <diamond>   directory containing the diamond executable
                        [DEFAULT: $PATH]
  --diamond-options <diamond_options>
                        options to be provided to the diamond software
                        [DEFAULT: "--top 1 --outfmt 6"]
  --evalue <1.0>        the evalue threshold to use with the translated search
                        [DEFAULT: 1.0]
  --protein-database <protein_database>
                        directory containing the protein database
                        [DEFAULT: /share/biocore/projects/Internal_Jessie_UCD/Workshops/Metagenomics_and_Metatranscriptomics/References/databases/uniref]
  --rapsearch <rapsearch>
                        directory containing the rapsearch executable
                        [DEFAULT: $PATH]
  --translated-alignment {usearch,rapsearch,diamond}
                        software to use for translated alignment
                        [DEFAULT: diamond]
  --translated-identity-threshold <Automatically: 50.0 or 80.0, Custom: 0.0-100.0>
                        identity threshold for translated alignments
                        [DEFAULT: Tuned automatically (based on uniref mode) unless a custom value is specified]
  --translated-query-coverage-threshold <90.0>
                        query coverage threshold for translated alignments
                        [DEFAULT: 90.0]
  --translated-subject-coverage-threshold <50.0>
                        subject coverage threshold for translated alignments
                        [DEFAULT: 50.0]
  --usearch <usearch>   directory containing the usearch executable
                        [DEFAULT: $PATH]

[5] Gene and pathway quantification:
  --gap-fill {on,off}   turn on/off the gap fill computation
                        [DEFAULT: on]
  --minpath {on,off}    turn on/off the minpath computation
                        [DEFAULT: on]
  --pathways {metacyc,unipathway}
                        the database to use for pathway computations
                        [DEFAULT: metacyc]
  --pathways-database <pathways_database.tsv>
                        mapping file (or files, at most two in a comma-delimited list) to use for pathway computations
                        [DEFAULT: metacyc database ]
  --xipe {on,off}       turn on/off the xipe computation
                        [DEFAULT: off]
  --annotation-gene-index <3>
                        the index of the gene in the sequence annotation
                        [DEFAULT: 3]
  --id-mapping <id_mapping.tsv>
                        id mapping file for alignments
                        [DEFAULT: alignment reference used]

[6] More output configuration:
  --remove-temp-output  remove temp output files
                        [DEFAULT: temp files are not removed]
  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        level of messages to display in log
                        [DEFAULT: DEBUG]
  --o-log <sample.log>  log file
                        [DEFAULT: temp/sample.log]
  --output-basename <sample_name>
                        the basename for the output files
                        [DEFAULT: input file basename]
  --output-format {tsv,biom}
                        the format of the output files
                        [DEFAULT: tsv]
  --output-max-decimals <10>
                        the number of decimals to output
                        [DEFAULT: 10]
  --remove-column-description-output
                        remove the description in the output column
                        [DEFAULT: output column includes description]
  --remove-stratified-output
                        remove stratification from output
                        [DEFAULT: output is stratified]