Biowulf High Performance Computing at the NIH
AdmixTools on Biowulf

ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.

The package contains 6 programs: Example files are in /usr/local/apps/AdmixTools/examples/

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load AdmixTools
[+] Loading AdmixTools 4.1 ...

[susanc@cn3144 examples]$ cp $AMT_DATA/* .
[susanc@cn3144 examples]$ expfit.sh rolloff-test-parfile.par
Running rexpfit.r 
Input file:  ASW_CEU_YRI
Output file:  expfit_ASW_CEU_YRI
Expfit logfile: expfit_ASW_CEU_YRI.flog
Output plot: expfit_ASW_CEU_YRI.pdf
 expfit.sh rolloff-test-parfile.par
Jackknife logfile: expfit_ASW_CEU_YRI.log
  
Jackknife summary: ASW_CEU_YRI.jin
Jackknife mean:          5.468
Jackknife std. err:      0.253
[denisovga@cn3145 test]$  expfit.sh rolloff-test-parfile.par
Running rexpfit.r 
Input file:  ASW_CEU_YRI
Output file:  expfit_ASW_CEU_YRI
Expfit logfile: expfit_ASW_CEU_YRI.flog
Output plot: expfit_ASW_CEU_YRI.pdf
Jackknife logfile: expfit_ASW_CEU_YRI.log

Jackknife summary: ASW_CEU_YRI.jin
Jackknife mean:          5.468
Jackknife std. err:      0.253

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
# this file is called admix.sh

module load AdmixTools

convertf -p par.EIGENSTRAT.PED

Submit this job using the Slurm sbatch command.

sbatch  [--mem=#] AdmixTools.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

rolloff -p rolloff1.par > rolloff1.log 2>&1
rolloff -p rolloff2.par > rolloff2.log 2>&1
rolloff -p rolloff3.par > rolloff3.log 2>&1

Submit this job using the swarm command.

swarm -f AdmixTools.swarm [-g #] --module AdmixTools
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module AdmixTools Loads the AdmixTools module for each subjob in the swarm