Structure-Teaching: Difference between revisions
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Also refer to [[Running Jobs on the teaching cluster]] | Also refer to [[Running Jobs on the teaching cluster]] | ||
The last version is at | The last version is at /apps/eb/structure/2.3.4-foss-2019b | ||
To use this program, please first load its module with | To use this program, please first load its module with | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
module load structure/2.3.4 | module load structure/2.3.4-foss-2019b | ||
</pre> | </pre> | ||
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cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
module load structure/2.3.4<br> | module load structure/2.3.4-foss-2019b<br> | ||
<br> | <br> | ||
structure [options] | structure [options] <br> | ||
</div> | </div> | ||
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Here is an example of job submission | Here is an example of job submission | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
sbatch ./sub.sh | |||
</pre> | </pre> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
module load structure/2.3.4 | module load structure/2.3.4-foss-2019b | ||
structure -h | structure -h | ||
---------------------------------------------------- | ---------------------------------------------------- | ||
Revision as of 22:20, 14 February 2021
Category
Bioinformatics
Program On
Teaching
Version
2.3.4
Author / Distributor
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 the teaching cluster
The last 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
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.
Installation
source code from Structure
System
64-bit Linux