MetaPhlAn4-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

4.0.3.1, 4.0.6, 4.1.1

Author / Distributor

Please see https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4

Description

From https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4: "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 StrainPhlAn, it is possible to perform accurate strain-level microbial profiling."

Running Program

Also refer to Running Jobs on Sapelo2

For more information on Environment Modules on Sapelo2 please see the Lmod page.

• Version 4.0.3.1 is installed as a singularity image at /apps/singularity-images/metaphlan4_4.0.3.1-path.sif

The bowtie2 database files for this version of MetaPhlAn are installed in /db/bowtie2/20230322. If you need to use the bowtie2 database files when running the metaphlan program, please use the --bowtie2db option to specify the location of these file, for example --bowtie2db /db/bowtie2/20230322.

The singularity command is available on all compute nodes, including the interactive nodes, and you don't need to load any modules to use it. This command is not available on the cluster login nodes. To see the help page for metaphlan on an interactive node, use the command

singularity exec /apps/singularity-images/metaphlan4_4.0.3.1-path.sif metaphlan -h

• Version 4.0.6 is installed as a singularity image at /apps/singularity-images/metaphlan4_4.0.6-path.sif

singularity exec /apps/singularity-images/metaphlan4_4.0.6-path.sif metaphlan -h

• Version 4.1.1 is installed as a module. To use this version, please first load the module with

ml MetaPhlAn/4.1.1-foss-2022a

The bowtie2 database files for this version of MetaPhlAn are installed in /db/bowtie2/20240912. If you need to use the bowtie2 database files when running the metaphlan program, please use the --bowtie2db option to specify the location of these file, for example --bowtie2db /db/bowtie2/20240912.

Sample job submission script (sub.sh) to run metaphlan version 4.0.3.1:

#!/bin/bash
#SBATCH --job-name=testmpa            # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=5gb                     # Job memory request
#SBATCH --time=02:00:00               # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out            # Standard output log
#SBATCH --error=%x.%j.err             # Standard error log

cd $SLURM_SUBMIT_DIR

singularity exec /apps/singularity-images/metaphlan4_4.0.3.1-path.sif metaphlan [options]

where [options] need to be replaced by the options (command and arguments) you want to use. If your analysis requires using the bowtie2 databases, please include the option --bowtie2db /db/bowtie2/20230322. Other parameters of the job, such as the maximum wall clock time, maximum memory, and the job name need to be modified appropriately as well.

Sample job submission script (sub.sh) to run metaphlan version 4.1.1:

#!/bin/bash
#SBATCH --job-name=testmpa            # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --ntasks=1                    # Run on a single CPU
#SBATCH --mem=5gb                     # Job memory request
#SBATCH --time=02:00:00               # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out            # Standard output log
#SBATCH --error=%x.%j.err             # Standard error log

cd $SLURM_SUBMIT_DIR

ml MetaPhlAn/4.1.1-foss-2022a

metaphlan [options]

where [options] need to be replaced by the options (command and arguments) you want to use. If your analysis requires using the bowtie2 databases, please include the option --bowtie2db /db/bowtie2/20240912. Other parameters of the job, such as the maximum wall clock time, maximum memory, and the job name need to be modified appropriately as well.

Submit the job to the queue with

sbatch sub.sh

Documentation

Please see https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4

Installation

Singularity images built from the docker container provided at https://hub.docker.com/r/gmtscience/metaphlan4/tags

singularity pull docker://gmtscience/metaphlan4:4.0.3.1

Version 4.1.1 was downloaded from https://github.com/biobakery/MetaPhlAn

System

64-bit Linux