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

References:

• D.H. Alexander, J. Novembre, and K. Lange. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655–1664, 2009.

• Admixture Main Site

• Module Name: admixture (see the modules page for more information)
• Multithreaded app (use -jX option)
• Example files in /usr/local/apps/admixture/example

Allocate an interactive session and run the program. Sample session (user input in bold):

[user@biowulf ~]$ sinteractive -c4 --mem=8g --gres=lscratch:10
salloc.exe: Pending job allocation 11085118
salloc.exe: job 11085118 queued and waiting for resources
salloc.exe: job 11085118 has been allocated resources
salloc.exe: Granted job allocation 11085118
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0848 are ready for job
srun: error: x11: no local DISPLAY defined, skipping
error: unable to open file /tmp/slurm-spank-x11.11085118.0
slurmstepd: error: x11: unable to read DISPLAY value

[user@cn0848 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn0848 11085118]$ cp /usr/local/apps/admixture/example/* .

[user@cn0848 11085118]$ module load admixture
[+] Loading admixture  1.3.0  on cn0848

[user@cn0848 11085118]$ admixture -help
****                   ADMIXTURE Version 1.3.0                  ****
****                    Copyright 2008-2015                     ****
****           David Alexander, Suyash Shringarpure,            ****
****                John  Novembre, Ken Lange                   ****
****                                                            ****
****                 Please cite our paper!                     ****
****   Information at www.genetics.ucla.edu/software/admixture  ****

Block size set manually to 0 SNPs
Usage: admixture <input file> <K>
See --help or manual for more advanced usage.

[user@cn0848 11085118]$ admixture hapmap3.bed 3 -j${SLURM_CPUS_PER_TASK}
****                   ADMIXTURE Version 1.3.0                  ****
****                    Copyright 2008-2015                     ****
****           David Alexander, Suyash Shringarpure,            ****
****                John  Novembre, Ken Lange                   ****
****                                                            ****
****                 Please cite our paper!                     ****
****   Information at www.genetics.ucla.edu/software/admixture  ****

Random seed: 43
Point estimation method: Block relaxation algorithm
Convergence acceleration algorithm: QuasiNewton, 3 secant conditions
Point estimation will terminate when objective function delta < 0.0001
Estimation of standard errors disabled; will compute point estimates only.
Size of G: 324x13928
Performing five EM steps to prime main algorithm
1 (EM)  Elapsed: 0.3    Loglikelihood: -4.38757e+06     (delta): 2.87325e+06
2 (EM)  Elapsed: 0.3    Loglikelihood: -4.25681e+06     (delta): 130762
3 (EM)  Elapsed: 0.299  Loglikelihood: -4.21622e+06     (delta): 40582.9
4 (EM)  Elapsed: 0.299  Loglikelihood: -4.19347e+06     (delta): 22748.2
5 (EM)  Elapsed: 0.299  Loglikelihood: -4.17881e+06     (delta): 14663.1
Initial loglikelihood: -4.17881e+06
Starting main algorithm
1 (QN/Block)    Elapsed: 0.723  Loglikelihood: -3.94775e+06     (delta): 231058
[...snip]
Summary:
Converged in 21 iterations (21.566 sec)
Loglikelihood: -3799887.171935
Fst divergences between estimated populations:
        Pop0    Pop1
Pop0
Pop1    0.163
Pop2    0.073   0.156
Writing output files.

[user@cn0848 11085118]$ exit
exit
salloc.exe: Relinquishing job allocation 11085118

[user@biowulf ~]$

Create a batch input file (e.g. admixture.sh). For example:

#!/bin/bash
set -e
module load admixture
admixture hapmap3.bed 3 -j${SLURM_CPUS_PER_TASK} > admixture.out

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=20g admixture.sh

Create a swarmfile (e.g. admixture.swarm). For example:

admixture hapmap3.bed 3 -j${SLURM_CPUS_PER_TASK} > admixture3.out
admixture hapmap20.bed 20 -j${SLURM_CPUS_PER_TASK} > admixture20.out
admixture hapmap1000.bed 1000 -j${SLURM_CPUS_PER_TASK} > admixture1000.out

Submit this job using the swarm command.

swarm -f admixture.swarm -g 20 -t 16 --module admixture