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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

ADMIXTURE

ADMIXTURE is a tool for fast maximum-likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but computes estimates much faster using a numerical optimization algorithm.

License

ADMIXTURE is free to use. It is distributed as a binary; see the ADMIXTURE home page for the license terms.

Available

  • Roihu: 1.4.0, via the bio-apps module.

Usage

ADMIXTURE is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the ADMIXTURE module:

module load bio-apps/v202603
module load admixture/1.4.0

ADMIXTURE takes a PLINK .bed (or .ped) genotype file and the number of assumed ancestral populations K. For example, to run with K = 3:

admixture input.bed 3

This produces the ancestry fractions (input.3.Q) and allele frequencies (input.3.P). ADMIXTURE can use multiple threads with the -j option.

Example batch script

#!/bin/bash
#SBATCH --job-name=admixture
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load admixture/1.4.0

admixture -j$SLURM_CPUS_PER_TASK input.bed 3

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information