Mothur
Mothur is a bioinformatics toolkit for the needs of the microbial ecology related data analysis.
License
Free to use and open source under GNU GPLv3.
Available
- Roihu-CPU: 1.48.0, via the
bio-appsmodule. - Chipster graphical user interface
Usage
Mothur is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Mothur module:
To see the available versions:
To run Mothur in interactive mode, use sinteractive. On the Roihu interactive partition each reserved core provides 1.875 GB of memory (up to 32 cores / 60 GB / 36 hours):
sinteractive --account <project> --cores 5
module load bio-apps/v202603
module load mothur/1.48.0
mothur
If your analyses take a long time, or you wish to use multiple cores, you should run Mothur as a batch job.
Start by collecting your Mothur commands into a command file to use Mothur in batch mode.
Once you have a working Mothur command file, you can launch Mothur jobs that take several days for completion, if needed.
Below is a sample Mothur batch job file. In this example, we assume that the Mothur commands are in the file my_mothur_task.txt.
#!/bin/bash
#SBATCH --account=<project>
#SBATCH --job-name=mothur
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=48:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=32G
module load bio-apps/v202603
module load mothur/1.48.0
mothur my_mothur_task.txt
If you want to use multiple cores, adjust the parameter --cpus-per-task. You must also adjust the processors parameter for each command in the Mothur command file accordingly. Note that only some Mothur commands can use multiple cores. Check the
documentation to check if the options for the command include processors.
Mothur jobs need to run inside a single node. You should check the scalability before submitting large jobs. Many Mothur tasks won't scale well beyond a few cores. Using too many cores may even make your job run slower.
The batch job script described above (in this case named as mothur_batch_job.sh) can be submitted to the batch job system
with the command:
See creating a batch job script for Roihu for more information about running batch jobs.