Structure-Teaching - Revision history

Shtsai at 01:37, 5 April 2026

2026-04-05T01:37:21Z

← Older revision		Revision as of 21:37, 4 April 2026
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	[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Teaching		Teaching

	=== Version ===		== Version ==
	2.3.4		2.3.4

	=== Author / Distributor ===		== Author / Distributor ==

	[http://web.stanford.edu/group/pritchardlab/structure.html Structure]		[http://web.stanford.edu/group/pritchardlab/structure.html Structure]

	=== Description ===		== 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. "		"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 [http://web.stanford.edu/group/pritchardlab/structure.html Structure]		More details are at [http://web.stanford.edu/group/pritchardlab/structure.html Structure]

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on the teaching cluster]]		Also refer to [[Running Jobs on the teaching cluster]]
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	source code from [http://web.stanford.edu/group/pritchardlab/structure.html Structure]		source code from [http://web.stanford.edu/group/pritchardlab/structure.html Structure]

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Shtsai: /* Documentation */

2026-01-09T20:54:21Z

Documentation

← Older revision		Revision as of 16:54, 9 January 2026
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	<pre class="gcommand">		<pre class="gcommand">

	module load structure/2.3.4-~~foss~~-~~2019b~~		module load structure/2.3.4-GCC-12.3.0
	structure -h		structure -h
	----------------------------------------------------		----------------------------------------------------

Shtsai: /* Running Program */

2026-01-09T20:53:35Z

Running Program

← Older revision		Revision as of 16:53, 9 January 2026
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	Also refer to [[Running Jobs on the teaching cluster]]		Also refer to [[Running Jobs on the teaching cluster]]

	The latest version is at /apps/eb/Structure/2.3.4-GCC-11.2.0		The latest version is at /apps/eb/Structure/2.3.4-GCC-12.3.0

	To use this program, please first load its module with<pre class="gcommand">		To use this program, please first load its module with<pre class="gcommand">
	module load Structure/2.3.4-GCC-11.2.0		module load Structure/2.3.4-GCC-12.3.0
	</pre>		</pre>

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	module load Structure/2.3.4-GCC-11.2.0<br>		module load Structure/2.3.4-GCC-12.3.0<br>
	<br>		<br>
	structure [options] <br>		structure [options] <br>

Chelsea: /* Running Program */

2024-05-14T13:40:27Z

Running Program

← Older revision		Revision as of 09:40, 14 May 2024
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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 /apps/eb/~~structure~~/2.3.4-~~foss~~-~~2019b~~		The latest version is at /apps/eb/Structure/2.3.4-GCC-11.2.0

	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-GCC-11.2.0
	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-~~foss~~-~~2019b~~<br>		module load Structure/2.3.4-GCC-11.2.0<br>
	<br>		<br>
	structure [options] <br>		structure [options] <br>

Shtsai: /* Documentation */

2021-02-15T02:20:57Z

Documentation

← Older revision		Revision as of 22:20, 14 February 2021
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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
	----------------------------------------------------		----------------------------------------------------

Shtsai: /* Running Program */

2021-02-15T02:20:28Z

Running Program

← Older revision		Revision as of 22:20, 14 February 2021
Line 23:		Line 23:
	Also refer to [[Running Jobs on the teaching cluster]]		Also refer to [[Running Jobs on the teaching cluster]]

	The last version is at /apps/eb/structure/2.3.4		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

Shtsai: /* Running Program */

2021-02-15T02:19:55Z

Running Program

← Older revision		Revision as of 22:19, 14 February 2021
Line 23:		Line 23:
	Also refer to [[Running Jobs on the teaching cluster]]		Also refer to [[Running Jobs on the teaching cluster]]

	The last version is at ~~/usr/local~~/apps/gb/structure/2.3.4		The last version is at /apps/eb/structure/2.3.4

	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] ~~1>job.out 2>job.err~~ <br>		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">
	~~qsub~~ ./sub.sh		sbatch ./sub.sh
	</pre>		</pre>

Shtsai: /* Running Program */

2019-02-14T14:17:18Z

Running Program

← Older revision		Revision as of 10:17, 14 February 2019
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	</div>		</div>

	In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.		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.

Shtsai: Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.3.4 === Author / Dist..."

2019-02-14T14:16:04Z

Created page with "Category:Teaching Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 2.3.4 === Author / Dist..."

New page

[[Category:Teaching]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Teaching

=== Version ===
2.3.4

=== Author / Distributor ===

[http://web.stanford.edu/group/pritchardlab/structure.html 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 [http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== Running Program ===

Also refer to [[Running Jobs on the teaching cluster]]

The last version is at /usr/local/apps/gb/structure/2.3.4

To use this program, please first load its module with
<pre class="gcommand">
module load structure/2.3.4
</pre>

Here is an example of a shell script sub.sh to run on at the batch queue:
<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=structurejob 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --mem=10gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=structurejob.%j.out 
<nowiki>#</nowiki>SBATCH --error=structurejob.%j.err 

cd $SLURM_SUBMIT_DIR 
module load structure/2.3.4 
 
structure [options] 1>job.out 2>job.err 
</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Here is an example of job submission
<pre class="gcommand">
qsub ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">

module load structure/2.3.4
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.
</pre>
[[#top|Back to Top]]

=== Installation ===

source code from [http://web.stanford.edu/group/pritchardlab/structure.html Structure]

=== System ===
64-bit Linux