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.
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