MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic sequencing data.
License
Free to use and open source under MIT License.
Available
- Roihu: 4.2.4 (module
py-metaphlan), via thebio-appsmodule.
Usage
MetaPhlAn is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the MetaPhlAn module:
You can check basic usage with the command:
Database
MetaPhlAn needs a marker database (the ChocoPhlAn-SGB Bowtie2 indexes) to run.
On Roihu a shared, read-only copy is provided centrally, and the py-metaphlan
module points MetaPhlAn at it automatically through the $METAPHLAN_DB_DIR
environment variable — so for the bundled database versions you do not need
to pass --db_dir.
The following database versions are available in the shared location:
mpa_vJan26_CHOCOPhlAnSGB_202605(latest)mpa_vJun23_CHOCOPhlAnSGB_202403
They sit side by side in one folder; choose which one to use with --index (its
value must be one of the versions listed above):
Using your own database
To use a version that is not in the shared location — or to let MetaPhlAn
download and build a fresh database — point --db_dir at a writable
directory of your own. An explicit --db_dir overrides $METAPHLAN_DB_DIR, and
because the shared copy is read-only MetaPhlAn cannot create a missing index
there.
For example, create a directory for the databases in your project's /scratch:
Databases can be pre-prepared with the --install option:
The database is quite big and downloading and building it can take some time.
By default the latest MetaPhlAn database is downloaded and built. You can request
a specific version with the --index parameter:
If the requested database is not found in the indicated writable location, it will be generated automatically.
A test input dataset for testing MetaPhlAn can be downloaded from the MetaPhlAn github site:
wget https://github.com/biobakery/MetaPhlAn/releases/download/4.0.2/SRS014476-Supragingival_plaque.fasta.gz
In this example the job is executed as an interactive job. On the Roihu interactive
partition each reserved core provides 1.875 GB of memory (up to 32 cores / 60 GB /
36 hours), so request the number of cores that gives you enough memory — here 8 cores
(about 15 GB):
sinteractive --account <project> --cores 8
module load bio-apps/v202603
module load py-metaphlan/4.2.4
metaphlan --nproc 8 --index mpa_vJan26_CHOCOPhlAnSGB_202605 SRS014476-Supragingival_plaque.fasta.gz --input_type fasta > SRS014476-Supragingival_plaque_profile.txt