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]