ILRI Research Computing

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====== metaphlan ======
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

===== Usage =====
Show all available versions:
<code>$ module avail metaphlan</code>

Load one version into your environment and run it:

<code>$ module load metaphlan/4.0.6
$ metaphlan -h</code>

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

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

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

===== Installation =====
Notes from the sysadmin during installation:

<code>$ 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</code>