MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

• Latest Version: 4.0.6
• Added: August, 2021
• Updated: July, 2023
• Link: https://github.com/biobakery/MetaPhlAn

Show all available versions:

$ module avail metaphlan

Load one version into your environment and run it:

$ module load metaphlan/4.0.6
$ metaphlan -h

Note: Please specify the number of CPU (processors) to use when you run metaphlan. For example:

$ metaphlan metagenome.fastq --input_type fastq --nproc 4 -o /var/scratch/profiled_metagenome.txt

The number of CPUs requested with the –nproc option should be the same as the number requested in your SBATCH, ie #SBATCH -n 4.

Notes from the sysadmin during installation:

$ module load python/3.9
$ sudo mkdir -p /export/apps/metaphlan/4.0.6
$ sudo chown aorth:aorth /export/apps/metaphlan/4.0.6
$ mkdir /export/apps/metaphlan/4.0.6/.venv
$ python -m venv /export/apps/metaphlan/4.0.6/.venv
$ source /export/apps/metaphlan/4.0.6/.venv/bin/activate
$ pip install --upgrade pip setuptools wheel
$ pip install metaphlan==4.0.6
$ module load bowtie2/2.5.0
$ metaphlan --install
$ sudo chown -R root:root /export/apps/metaphlan/4.0.6