metaphlan-software
Table of Contents
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: 3.0.13
- Added: August, 2021
Usage
Show all available versions of metaphlan:
$ module avail metaphlan
Load one version into your environment and run it:
$ module load metaphlan/3.0.13 $ 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
.
Installation
Notes from the sysadmin during installation:
$ sudo mkdir -p /export/apps/metaphlan/3.0.13 $ sudo chown aorth:aorth /export/apps/metaphlan/3.0.13 $ module load python/3.8 $ python3 -m venv /export/apps/metaphlan/3.0.13 $ source /export/apps/metaphlan/3.0.13/bin/activate $ pip install --upgrade setuptools pip $ pip install metaphlan==3.0.13 $ metaphlan --install $ sudo chown -R root:root /export/apps/metaphlan/3.0.13
metaphlan-software.txt · Last modified: 2021/08/29 08:12 by aorth