Error when running HUMAnN tutorial

Microbial community profiling HUMAnN
3

Thank you for your response, Eric—it got me to the right answer. In case it helps other new users, here are the commands that worked for me:

Installation

conda create --name biobakery4 python=3.12
conda activate biobakery4
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels biobakery
conda install humann=4.0.0a1 metaphlan=4.1 -c biobakery
metaphlan --install --index mpa_vOct22_CHOCOPhlAnSGB_202403

This installs the correct version of MetaPhlAn (4.1); the one installed by default doesn’t work. It also installs the correct version of the database (mpa_vOct22_CHOCOPhlAnSGB_202403).

Running tutorial data

conda activate biobakery4
metaphlan demo.fastq.gz --input_type fastq > demo.tsv -x mpa_vOct22_CHOCOPhlAnSGB_202403 -t rel_ab_w_read_stats
humann -i demo.fastq.gz --taxonomic-profile demo.tsv --output demo

This runs MetaPhlAn and HUMAnN sequentially through two separate commands. They are run in a single command in the tutorial, but that didn’t work for me. It also uses the correct version of the database (mpa_vOct22_CHOCOPhlAnSGB_202403).

I look forward to using MetaPhlAn and HUMAnN in a tool my lab is developing.

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