Mothur 1.42.3¶

Basic Information¶

Deploy date: 24 January 2019
Official Website: https://www.mothur.org
License: GNU General Public License
Installed on: Apolo II

Installation¶

This entry covers the entire process performed for the installation and configuration of Mothur.

Usage¶

This section describes the method to submit jobs with the resource manager SLURM.

Load the necessary environment.

module load mothur/1.42.1_intel-2017_update-1

Run Mothur with SLURM.

An example with AmazonData.zip:

mothur.sh¶

#!/bin/bash                                                                                                          

#SBATCH --job-name=serial_test       # Job name                                                                      
#SBATCH --mail-type=ALL         # Mail notification                                                                  
#SBATCH --mail-user=<user>@<domain>  # User Email                                                                    
#SBATCH --output=mothur-%j.out # Stdout (%j expands to jobId)                                                        
#SBATCH --error=mothur-%j.err  # Stderr (%j expands to jobId)                                                        
#SBATCH --ntasks=1                   # Number of tasks (processes)                                                   
#SBATCH --time=01:00                 # Walltime                                                                      
#SBATCH --partition=longjobs         # Partition                                                                     


##### ENVIRONMENT CREATION #####                                                                                     

module load mothur/1.42.1_intel-2017_update-1

##### JOB COMMANDS ####                                                                                              

mothur "#read.dist(phylip=98_sq_phylip_amazon.dist, cutoff=0.1); cluster(); collect.single(); rarefaction.single()"

Authors¶

Manuela Carrasco Pinzón <mcarras1@eafit.edu.co>