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
module spider mothur
module load mothur/1.48.0
sinteractive --account=project_1234567 -m 8000 module load mothur mothur
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.
#!/bin/bash #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: mothur_batch_job.sh) can be submitted to the batch job system with command: