Structure-Sapelo2 - Revision history

Shtsai at 01:36, 5 April 2026

2026-04-05T01:36:45Z

← Older revision		Revision as of 21:36, 4 April 2026
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	[[Category:~~Teaching~~]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

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

	Sapelo2		Sapelo2

	=== 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 Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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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

Chelsea: /* Running Program */

2024-05-14T13:39:38Z

Running Program

← Older revision		Revision as of 09:39, 14 May 2024
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	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]

	The latest 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-~~foss~~-~~2019b~~		module load Structure/2.3.4-GCC-11.2.0
	</pre>		</pre>

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	<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br><nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br><nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br><nowiki>#</nowiki>SBATCH --output=<u>structurejob</u>.%j.out<br><nowiki>#</nowiki>SBATCH --error=<u>structurejob</u>.%j.err<br>		<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br><nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br><nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br><nowiki>#</nowiki>SBATCH --output=<u>structurejob</u>.%j.out<br><nowiki>#</nowiki>SBATCH --error=<u>structurejob</u>.%j.err<br>

	cd $SLURM_SUBMIT_DIR<br>module load ~~structure~~/2.3.4-~~foss~~-~~2019b~~<br>		cd $SLURM_SUBMIT_DIR<br>module load Structure/2.3.4-GCC-11.2.0<br>

	structure [options]		structure [options]

Keeko: added info about mainparams and extraparams file

2022-02-01T01:24:59Z

added info about mainparams and extraparams file

← Older revision		Revision as of 21:24, 31 January 2022
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	module load structure/2.3.4-foss-2019b		module load structure/2.3.4-foss-2019b
	</pre>		</pre>

			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:

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

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

Keeko: minor page formatting

2022-02-01T01:16:43Z

minor page formatting

← Older revision		Revision as of 21:16, 31 January 2022
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	=== Program On ===		=== Program On ===

	~~Teaching~~		Sapelo2

	=== Version ===		=== Version ===
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	=== Running Program ===		=== Running Program ===

	Also refer to [[Running Jobs on ~~the teaching cluster~~]]		Also refer to [[Running Jobs on Sapelo2]]

	The ~~last~~ version is at /apps/eb/structure/2.3.4-foss-2019b		The latest 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
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	Here is an example of a shell script sub.sh to run on at the batch queue:		Here is an example of a shell script sub.sh to run on at the batch queue:
	<div class="gscript2">		<div class="gscript2">
	<nowiki>#</nowiki>!/bin/bash<br>		<nowiki>#</nowiki>!/bin/bash<br><nowiki>#</nowiki>SBATCH --job-name=<u>structurejob</u><br><nowiki>#</nowiki>SBATCH --partition=batch<br><nowiki>#</nowiki>SBATCH --mail-type=ALL<br><nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u>
	<nowiki>#</nowiki>SBATCH --job-name=<u>structurejob</u><br>
	<nowiki>#</nowiki>SBATCH --partition=batch<br>		<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br><nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br><nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br><nowiki>#</nowiki>SBATCH --output=<u>structurejob</u>.%j.out<br><nowiki>#</nowiki>SBATCH --error=<u>structurejob</u>.%j.err<br>
	<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>
	<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u>~~<br>~~		cd $SLURM_SUBMIT_DIR<br>module load structure/2.3.4-foss-2019b<br>
	<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br>
	<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br>		structure [options]
	<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>
	<nowiki>#</nowiki>SBATCH --output=<u>structurejob</u>.%j.out<br>
	<nowiki>#</nowiki>SBATCH --error=<u>structurejob</u>.%j.err<br>

	cd $SLURM_SUBMIT_DIR<br>
	module load structure/2.3.4-foss-2019b<br>
	~~<br>~~
	structure [options] ~~<br>~~
	</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. And [options] should be replaced by any options you want to use.		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		Here is an example of job submission

Keeko: created STRUCTURE page

2022-02-01T01:12:31Z

created STRUCTURE page

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 /apps/eb/structure/2.3.4-foss-2019b

To use this program, please first load its module with
<pre class="gcommand">
module load structure/2.3.4-foss-2019b
</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-foss-2019b 
 
structure [options] 
</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. And [options] should be replaced by any options you want to use.

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

=== Documentation ===

<pre class="gcommand">

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.
</pre>
[[#top|Back to Top]]

=== Installation ===

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

=== System ===
64-bit Linux