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Mothur is a bioinformatics toolkit for the needs of the microbial ecology related data analysis.


Free to use and open source under GNU GPLv3.


Version on CSC's Servers

  • Puhti: 1.48.0
  • Chipster graphical user interface


To initialize the default version of Mothur in Puhti use:

module load mothur
To see all available versions:
module spider mothur
To load a specific version:
module load mothur/1.48.0
To tun Mothur in interactive mode, use sinteractive.
sinteractive --account=project_1234567 -m 8000
module load 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 can take several days, if needed.

Below is a sample Mothur batch job file. In this example we assume that the Mothur commands are in file: my_mothur_task.txt.

#SBATCH --account=project_1234567
#SBATCH --job-name=mothur
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=32G
#SBATCH --time=48:00:00
#SBATCH --partition=small

module load mothur
mothur my_mothur_task.txt

If you want to use multiple cores, adjust 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. Please check the documentation.

Mothur jobs need to run inside a single node, so the maximum number of cores you can use in Puhti is 40. You should check the scalability before submitting large jobs. Many Mothur tasks won't scale well beyond a few cores. Using too many core may even make you job run slower.

The batch job script described above (in this case named as: can be submitted to the batch job system with command:

See the Puhti user guide for more information about running batch jobs.



Last update: October 10, 2022