MetaPhlAn4-Sapelo2: Difference between revisions
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Sapelo2 | Sapelo2 | ||
=== Version === | === Version === | ||
4.0.3.1, 4.0.6 | 4.0.3.1, 4.0.6, 4.1.1 | ||
===Author / Distributor=== | ===Author / Distributor=== | ||
Please see https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4 | Please see https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4 | ||
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singularity exec /apps/singularity-images/metaphlan4_4.0.3.1-path.sif metaphlan -h | singularity exec /apps/singularity-images/metaphlan4_4.0.3.1-path.sif metaphlan -h | ||
</pre> | </pre> | ||
*Version 4.0.6 is installed as a singularity image at /apps/singularity-images/metaphlan4_4.0.6-path.sif | |||
<pre class="gcommand"> | |||
singularity exec /apps/singularity-images/metaphlan4_4.0.6-path.sif metaphlan -h | |||
</pre> | |||
*Version 4.1.1 is installed as a module. To use this version, please first load the module with | |||
<pre class="gcommand"> | |||
ml MetaPhlAn/4.1.1-foss-2022a | |||
</pre> | |||
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: | Sample job submission script (sub.sh) to run metaphlan version 4.0.3.1: | ||
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</pre> | </pre> | ||
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. | 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: | |||
<pre class="gscript"> | |||
#!/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] | |||
</pre> | |||
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 | Submit the job to the queue with | ||
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singularity pull docker://gmtscience/metaphlan4:4.0.3.1 | singularity pull docker://gmtscience/metaphlan4:4.0.3.1 | ||
</pre> | </pre> | ||
Version 4.1.1 was downloaded from https://github.com/biobakery/MetaPhlAn | |||
=== System === | === System === | ||
64-bit Linux | 64-bit Linux | ||
Latest revision as of 09:15, 13 September 2024
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