Hi Francesco,
I run the following code, but it doesn’t work:
(py37) [zhangwenping@localhost try_humann]$ humann --input /data/liying_metagenome/clean_data_liying/SRR5130527_paired.1.fastq --output try_SRR5130527_paired.1 --metaphlan-options -x mpa_v30_CHOCOPhlAn_201901 --bowtie2db /data/xmjd/miniconda2/envs/py37/lib/python3.7/site-packages/metaphlan/metaphlan_databases/
usage: humann [-h] [–version] [-v] [-r] [–bypass-prescreen]
[–bypass-nucleotide-index] [–bypass-translated-search]
[–bypass-nucleotide-search] -i <input.fastq> -o
[–nucleotide-database <nucleotide_database>]
[–annotation-gene-index <3>]
[–protein-database <protein_database>] [–evalue <1.0>]
[–search-mode {uniref50,uniref90}] [–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 ] [–usearch ]
[–rapsearch ] [–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: error: argument --metaphlan-options: expected one argument