MetaPhlAn4-Sapelo2 - Revision history

Shtsai at 01:06, 5 April 2026

2026-04-05T01:06:45Z

← Older revision		Revision as of 21:06, 4 April 2026
Line 1:		Line 1:
	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==
	Bioinformatics		Bioinformatics
	=== Program On ===		== Program On ==
	Sapelo2		Sapelo2
	=== Version ===		== Version ==
	4.0.3.1, 4.0.6, 4.1.1		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
	===Description===		==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."		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 ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
Line 89:		Line 89:
	</pre>		</pre>

	=== Documentation ===		== Documentation ==

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

	=== Installation ===		== Installation ==

	Singularity images built from the docker container provided at https://hub.docker.com/r/gmtscience/metaphlan4/tags		Singularity images built from the docker container provided at https://hub.docker.com/r/gmtscience/metaphlan4/tags
Line 102:		Line 102:
	Version 4.1.1 was downloaded from https://github.com/biobakery/MetaPhlAn		Version 4.1.1 was downloaded from https://github.com/biobakery/MetaPhlAn

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai: /* Running Program */

2024-09-13T14:15:35Z

Running Program

← Older revision		Revision as of 10:15, 13 September 2024
Line 37:		Line 37:
	ml MetaPhlAn/4.1.1-foss-2022a		ml MetaPhlAn/4.1.1-foss-2022a
	</pre>		</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'''.

Shtsai at 14:14, 13 September 2024

2024-09-13T14:14:32Z

@@ Line 5: / Line 5: @@
 Sapelo2
 === Version ===
-.0.3.1, 4.0.6
+.0.3.1, 4.0.6, 4.1.1
 ===Author / Distributor===
 Please see https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4
@@ Line 25: / Line 25: @@
 singularity exec /apps/singularity-images/metaphlan4_4.0.3.1-path.sif metaphlan -h
 </pre>
 Sample job submission script (sub.sh) to run metaphlan version 4.0.3.1:
@@ Line 44: / Line 57: @@
 </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.
 Submit the job to the queue with
@@ Line 60: / Line 96: @@
 singularity pull docker://gmtscience/metaphlan4:4.0.3.1
 </pre>
 === System ===
 -bit Linux

Chelsea: /* Version */

2024-05-13T16:34:39Z

Version

← Older revision		Revision as of 12:34, 13 May 2024
Line 5:		Line 5:
	Sapelo2		Sapelo2
	=== Version ===		=== Version ===
	4.0.3.1		4.0.3.1, 4.0.6
	===Author / Distributor===		===Author / Distributor===
	Please see https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4		Please see https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4

Shtsai: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 4.0.3.1 ===Author / Distribut..."

2023-03-22T18:44:55Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 4.0.3.1 ===Author / Distribut..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===
Bioinformatics
=== Program On ===
Sapelo2
=== Version ===
4.0.3.1
===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

<pre class="gcommand">
singularity exec /apps/singularity-images/metaphlan4_4.0.3.1-path.sif metaphlan -h
</pre>

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

<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

singularity exec /apps/singularity-images/metaphlan4_4.0.3.1-path.sif 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/bowtie2/20230322'''. 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.

Submit the job to the queue with
<pre class="gcommand">
sbatch sub.sh
</pre>

=== 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
<pre class="gcommand">
singularity pull docker://gmtscience/metaphlan4:4.0.3.1
</pre>

=== System ===
64-bit Linux