Humann3

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

HUMAnN : HMP Unified Metabolic Analysis Network 2

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -v, --verbose         additional output is printed
  -r, --resume          bypass commands if the output files exist
  --bypass-prescreen    bypass the prescreen step and run on the full ChocoPhlAn database
  --bypass-nucleotide-index
                        bypass the nucleotide index step and run on the indexed ChocoPhlAn database
  --bypass-translated-search
                        bypass the translated search step
  --bypass-nucleotide-search
                        bypass the nucleotide search steps
  -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]
  --nucleotide-database <nucleotide_database>
                        directory containing the nucleotide database
                        [DEFAULT: /usr/local/lib/python3.6/dist-packages/humann/data/chocophlan_DEMO]
  --annotation-gene-index <3>
                        the index of the gene in the sequence annotation
                        [DEFAULT: 3]
  --protein-database <protein_database>
                        directory containing the protein database
                        [DEFAULT: /usr/local/lib/python3.6/dist-packages/humann/data/uniref_DEMO]
  --evalue <1.0>        the evalue threshold to use with the translated search
                        [DEFAULT: 1.0]
  --search-mode {uniref50,uniref90}
                        search for uniref50 or uniref90 gene families
                        [DEFAULT: based on translated database selected]
  --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"]
  --diamond-options <diamond_options>
                        options to be provided to the diamond software
                        [DEFAULT: "--top 1 --outfmt 6"]
  --bowtie-options <bowtie_options>
                        options to be provided to the bowtie software
                        [DEFAULT: "--very-sensitive"]
  --o-log <sample.log>  log file
                        [DEFAULT: temp/sample.log]
  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        level of messages to display in log
                        [DEFAULT: DEBUG]
  --remove-temp-output  remove temp output files
                        [DEFAULT: temp files are not removed]
  --threads <1>         number of threads/processes
                        [DEFAULT: 1]
  --prescreen-threshold <0.01>
                        minimum percentage of reads matching a species
                        [DEFAULT: 0.01]
  --nucleotide-identity-threshold <0.0>
                        identity threshold for nuclotide alignments
                        [DEFAULT: 0.0]
  --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-subject-coverage-threshold <50.0>
                        subject coverage threshold for translated alignments
                        [DEFAULT: 50.0]
  --nucleotide-subject-coverage-threshold <50.0>
                        subject coverage threshold for nucleotide alignments
                        [DEFAULT: 50.0]
  --translated-query-coverage-threshold <90.0>
                        query coverage threshold for translated alignments
                        [DEFAULT: 90.0]
  --nucleotide-query-coverage-threshold <90.0>
                        query coverage threshold for nucleotide alignments
                        [DEFAULT: 90.0]
  --bowtie2 <bowtie2>   directory containing the bowtie2 executable
                        [DEFAULT: $PATH]
  --usearch <usearch>   directory containing the usearch executable
                        [DEFAULT: $PATH]
  --rapsearch <rapsearch>
                        directory containing the rapsearch executable
                        [DEFAULT: $PATH]
  --diamond <diamond>   directory containing the diamond executable
                        [DEFAULT: $PATH]
  --taxonomic-profile <taxonomic_profile.tsv>
                        a taxonomic profile (the output file created by metaphlan)
                        [DEFAULT: file will be created]
  --id-mapping <id_mapping.tsv>
                        id mapping file for alignments
                        [DEFAULT: alignment reference used]
  --translated-alignment {usearch,rapsearch,diamond}
                        software to use for translated alignment
                        [DEFAULT: diamond]
  --xipe {on,off}       turn on/off the xipe computation
                        [DEFAULT: off]
  --minpath {on,off}    turn on/off the minpath computation
                        [DEFAULT: on]
  --pick-frames {on,off}
                        turn on/off the pick_frames computation
                        [DEFAULT: off]
  --gap-fill {on,off}   turn on/off the gap fill computation
                        [DEFAULT: on]
  --output-format {tsv,biom}
                        the format of the output files
                        [DEFAULT: tsv]
  --output-max-decimals <10>
                        the number of decimals to output
                        [DEFAULT: 10]
  --output-basename <sample_name>
                        the basename for the output files
                        [DEFAULT: input file basename]
  --remove-stratified-output
                        remove stratification from output
                        [DEFAULT: output is stratified]
  --remove-column-description-output
                        remove the description in the output column
                        [DEFAULT: output column includes description]
  --input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom}
                        the format of the input file
                        [DEFAULT: format identified by software]
  --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 ]
  --pathways {metacyc,unipathway}
                        the database to use for pathway computations
                        [DEFAULT: metacyc]
  --memory-use {minimum,maximum}
                        the amount of memory to use
                        [DEFAULT: minimum]

usage: humann [-h] [--version] [-v] [-r] [--bypass-prescreen] [--bypass-nucleotide-index] [--bypass-translated-search] [--bypass-nucleotide-search] -i <input.fastq> -o <output> [--nucleotide-database <nucleotide_database>] [--annotation-gene-index <3>] [--protein-database <protein_database>] [--evalue <1.0>] [--search-mode {uniref50,uniref90}] [--metaphlan <metaphlan>] [--metaphlan-options <metaphlan_options>] [--diamond-options <diamond_options>] [--bowtie-options <bowtie_options>] [--o-log <sample.log>] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--remove-temp-output] [--threads <1>] [--prescreen-threshold <0.01>] [--nucleotide-identity-threshold <0.0>] [--translated-identity-threshold <Automatically: 50.0 or 80.0, Custom: 0.0-100.0>] [--translated-subject-coverage-threshold <50.0>] [--nucleotide-subject-coverage-threshold <50.0>] [--translated-query-coverage-threshold <90.0>] [--nucleotide-query-coverage-threshold <90.0>] [--bowtie2 <bowtie2>] [--usearch <usearch>] [--rapsearch <rapsearch>] [--diamond <diamond>] [--taxonomic-profile <taxonomic_profile.tsv>] [--id-mapping <id_mapping.tsv>] [--translated-alignment {usearch,rapsearch,diamond}] [--xipe {on,off}] [--minpath {on,off}] [--pick-frames {on,off}] [--gap-fill {on,off}] [--output-format {tsv,biom}] [--output-max-decimals <10>] [--output-basename <sample_name>] [--remove-stratified-output] [--remove-column-description-output] [--input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom}] [--pathways-database <pathways_database.tsv>] [--pathways {metacyc,unipathway}] [--memory-use {minimum,maximum}] HUMAnN : HMP Unified Metabolic Analysis Network 2 optional arguments: -h, --help show this help message and exit --version show program's version number and exit -v, --verbose additional output is printed -r, --resume bypass commands if the output files exist --bypass-prescreen bypass the prescreen step and run on the full ChocoPhlAn database --bypass-nucleotide-index bypass the nucleotide index step and run on the indexed ChocoPhlAn database --bypass-translated-search bypass the translated search step --bypass-nucleotide-search bypass the nucleotide search steps -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] --nucleotide-database <nucleotide_database> directory containing the nucleotide database [DEFAULT: /usr/local/lib/python3.6/dist-packages/humann/data/chocophlan_DEMO] --annotation-gene-index <3> the index of the gene in the sequence annotation [DEFAULT: 3] --protein-database <protein_database> directory containing the protein database [DEFAULT: /usr/local/lib/python3.6/dist-packages/humann/data/uniref_DEMO] --evalue <1.0> the evalue threshold to use with the translated search [DEFAULT: 1.0] --search-mode {uniref50,uniref90} search for uniref50 or uniref90 gene families [DEFAULT: based on translated database selected] --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"] --diamond-options <diamond_options> options to be provided to the diamond software [DEFAULT: "--top 1 --outfmt 6"] --bowtie-options <bowtie_options> options to be provided to the bowtie software [DEFAULT: "--very-sensitive"] --o-log <sample.log> log file [DEFAULT: temp/sample.log] --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} level of messages to display in log [DEFAULT: DEBUG] --remove-temp-output remove temp output files [DEFAULT: temp files are not removed] --threads <1> number of threads/processes [DEFAULT: 1] --prescreen-threshold <0.01> minimum percentage of reads matching a species [DEFAULT: 0.01] --nucleotide-identity-threshold <0.0> identity threshold for nuclotide alignments [DEFAULT: 0.0] --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-subject-coverage-threshold <50.0> subject coverage threshold for translated alignments [DEFAULT: 50.0] --nucleotide-subject-coverage-threshold <50.0> subject coverage threshold for nucleotide alignments [DEFAULT: 50.0] --translated-query-coverage-threshold <90.0> query coverage threshold for translated alignments [DEFAULT: 90.0] --nucleotide-query-coverage-threshold <90.0> query coverage threshold for nucleotide alignments [DEFAULT: 90.0] --bowtie2 <bowtie2> directory containing the bowtie2 executable [DEFAULT: $PATH] --usearch <usearch> directory containing the usearch executable [DEFAULT: $PATH] --rapsearch <rapsearch> directory containing the rapsearch executable [DEFAULT: $PATH] --diamond <diamond> directory containing the diamond executable [DEFAULT: $PATH] --taxonomic-profile <taxonomic_profile.tsv> a taxonomic profile (the output file created by metaphlan) [DEFAULT: file will be created] --id-mapping <id_mapping.tsv> id mapping file for alignments [DEFAULT: alignment reference used] --translated-alignment {usearch,rapsearch,diamond} software to use for translated alignment [DEFAULT: diamond] --xipe {on,off} turn on/off the xipe computation [DEFAULT: off] --minpath {on,off} turn on/off the minpath computation [DEFAULT: on] --pick-frames {on,off} turn on/off the pick_frames computation [DEFAULT: off] --gap-fill {on,off} turn on/off the gap fill computation [DEFAULT: on] --output-format {tsv,biom} the format of the output files [DEFAULT: tsv] --output-max-decimals <10> the number of decimals to output [DEFAULT: 10] --output-basename <sample_name> the basename for the output files [DEFAULT: input file basename] --remove-stratified-output remove stratification from output [DEFAULT: output is stratified] --remove-column-description-output remove the description in the output column [DEFAULT: output column includes description] --input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom} the format of the input file [DEFAULT: format identified by software] --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 ] --pathways {metacyc,unipathway} the database to use for pathway computations [DEFAULT: metacyc] --memory-use {minimum,maximum} the amount of memory to use [DEFAULT: minimum]