I am a new user and get an error when running the HUMAnN tutorial. Specifically, running
humann --input demo.fastq.gz --output demo_fastq
results in
metaphlan: error: unrecognized arguments: --bowtie2out .../humann/demo_fastq/demo_humann_temp/demo_metaphlan_bowtie2.txt
The tutorial installs MetaPhlAn version 4.2.2 (4 Jun 2025) and humann v3.9, and the error may be related to this issue or possibly this one.
Can you please indicate which commands in the tutorial need to be updated? Thank you for your help.