Structure-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

2.3.4

Author / Distributor

Structure

Description

"The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. " More details are at Structure

Running Program

Also refer to Running Jobs on Sapelo2

The latest version is at /apps/eb/structure/2.3.4-foss-2019b

To use this program, please first load its module with

module load structure/2.3.4-foss-2019b

To run STUCTURE you will need both a mainparams file and an extraparams file. These two files contain program parameters which are set by the user, and are read every time the program executes. Make sure both of those files are in your working directory when you use structure. You can also specify those files with the -m (mainparams) and -e (extraparams) options to the structure command.

More about the mainparams and extraparams file can be found here:

https://web.stanford.edu/group/pritchardlab/software/readme/node32.html

Examples of the mainparams file and extraparams file which you can use as templates can be found at /apps/eb/structure/2.3.4-foss-2019b/mainparams and /apps/eb/structure/2.3.4-foss-2019b/extraparams respectively.

Here is an example of a shell script sub.sh to run on at the batch queue:

#!/bin/bash
#SBATCH --job-name=structurejob
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu

#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=structurejob.%j.out
#SBATCH --error=structurejob.%j.err

cd $SLURM_SUBMIT_DIR
module load structure/2.3.4-foss-2019b

structure [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. And [options] should be replaced by any options you want to use.

Here is an example of job submission

sbatch  ./sub.sh 

Documentation

module load structure/2.3.4-foss-2019b
structure -h
----------------------------------------------------
STRUCTURE by Pritchard, Stephens and Donnelly (2000)
     and Falush, Stephens and Pritchard (2003)
       Code by Pritchard, Falush and Hubisz
             Version 2.3.4 (Jul 2012)
----------------------------------------------------


Reading file "mainparams".
datafile is
infile
Reading file "extraparams".
Note: RANDOMIZE is set to 1. The random number generator will be initialized using the system clock, ignoring any specified value of SEED.
Unable to open the file infile.

Exiting the program due to error(s) listed above.

Back to Top

Installation

source code from Structure

System

64-bit Linux