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mothur

Description

mothur is a tool for analyzing 16S rRNA gene sequences generated on multiple platforms as part of microbial ecology projects.

How To Use

There are multiple versions of mothur available. An easy way of selecting the version is to use modules. To see the modules available, type

module avail mothur

To select a module, type

module load mothur/[ver]

where [ver] is the version of choice. This will set your $PATH variable, allowing easy access to the two executable commands, mothur and uchime.

Use on Helix

To run an example, first symlink these files to your current working directory and start mothur:

[helix]$ ln -s /usr/local/apps/mothur/examples/MiSeq_SOP/* .
[helix]$ mothur
...
mothur > 

mothur is an inherently interactive application, and expects commands at the prompt.

mothur > make.contigs(file=stability.files, processors=8)
...
mothur > summary.seqs(fasta=stability.trim.contigs.fasta)


Using 8 processors.

                Start   End     NBases  Ambigs  Polymer NumSeqs
Minimum:        1       248     248     0       3       1
2.5%-tile:      1       252     252     0       3       3810
25%-tile:       1       252     252     0       4       38091
Median:         1       252     252     0       4       76181
75%-tile:       1       253     253     0       5       114271
97.5%-tile:     1       253     253     6       6       148552
Maximum:        1       503     502     249     243     152360
Mean:   1       252.811 252.811 0.697867        4.44854
# of Seqs:      152360

Output File Names: 
stability.trim.contigs.summary


mothur > 

See http://www.mothur.org/wiki/MiSeq_SOP for the rest of this tutorial.

Use on Biowulf

The same example run on Helix interactively can be run in batch mode using the stability.batch file.

#----- This file is MiSeq_SOP.sh -----#
#!/bin/bash

# Set the environment
module load mothur

# Untar the example data files
tar xzf $MOTHUREXAMPLES/MiSeq_SOP.tgz
cd MiSeq_SOP

# Run the batch script
mothur stability.batch

Because the stability.batch file requires 8 processors, this job must request at least 8 processors:

[biowulf]$ sbatch --cpus-per-task=8 --job-name=MiSeq_SOP --output=MiSeq_SOP.out MiSeq_SOP.sh

Documentation