mothur
Mothur is an open source software package for bioinformatics data processing. The package is frequently used in the analysis of DNA from uncultured microbes.
Detailed information about Mothur can be found here: https://mothur.org
Link to section 'Versions' of 'mothur' Versions
- 1.46.0
- 1.47.0
- 1.48.0
Link to section 'Commands' of 'mothur' Commands
- mothur
Link to section 'Module' of 'mothur' Module
You can load the modules by:
module load biocontainers
module load mothur/1.47.0
Link to section 'Interactive job' of 'mothur' Interactive job
To run mothur interactively on our clusters:
(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers mothur/1.47.0
(base) UserID@bell-a008:~ $ mothur
Linux version
Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
by
Patrick D. Schloss
Department of Microbiology & Immunology
University of Michigan
http://www.mothur.org
When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.
Distributed under the GNU General Public License
Type 'help()' for information on the commands that are available
For questions and analysis support, please visit our forum at https://forum.mothur.org
Type 'quit()' to exit program
[NOTE]: Setting random seed to 19760620.
Interactive Mode
mothur > align.seqs(help)
mothur > quit()
Link to section 'Batch job' of 'mothur' Batch job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To submit a sbatch job on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=mothur
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers mothur/1.47.0
mothur batch_file