humann2: error: argument -o/--output: expected one argument

[Christopher Poulton]

Hi Team

Testing out the demo run: humann2 --input examples/demo.fastq --output $OUTPUT_DIR

I'm getting this error message: humann2: error: argument -o/--output: expected one argument

Can some one please tell me what this means.

[Christopher Poulton]

OUTPUT_DIR
usage: humann2 [-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 <8>]
               [--protein-database <protein_database>] [--evalue <1.0>]
               [--search-mode {uniref50,uniref90}] [--metaphlan <metaphlan>]
               [--metaphlan-options <metaphlan_options>]
               [--o-log <sample.log>]
               [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
               [--remove-temp-output] [--threads <1>]
               [--prescreen-threshold <0.01>] [--identity-threshold <50.0>]
               [--translated-subject-coverage-threshold <50.0>]
               [--translated-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}]

[Lauren McIver]

Hi Christopher,

HUMAnN2 expects an output folder as one of the arguments. If you replace $OUTPUT_DIR with the folder you would like humann2 to write to, it should resolve the error message (ie. "humann2 --input examples/demo.fastq --output humann2_output_folder"). 

Thanks!

Lauren