Structure-Sapelo2: Difference between revisions
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=== Program On === | === Program On === | ||
Sapelo2 | |||
=== Version === | === Version === | ||
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=== Running Program === | === Running Program === | ||
Also refer to [[Running Jobs on | Also refer to [[Running Jobs on Sapelo2]] | ||
The | 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> | 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> | |||
structure [options] | |||
</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 | ||
Revision as of 20:16, 31 January 2022
Category
Bioinformatics
Program On
Sapelo2
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 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
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