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AdmixTools on NIH HPC Systems

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/

On Helix

Sample session:

[susanc@helix~]$ module load AdmixTools

[susanc@helix~]$ cp -r /usr/local/apps/AdmixTools/3.0/convertf .  ; cd convertf

[susanc@helix~]$ convertf -p par.EIGENSTRAT.PED
## convertf version: 4480
parameter file: par.EIGENSTRAT.PED
genotypename: example.eigenstratgeno
snpname: example.snp
indivname: example.ind
outputformat: PED
genotypeoutname: example.ped
snpoutname: example.pedsnp
indivoutname: example.pedind
numvalidind:      5  maxmiss:  5001
ped output
##end of convertf run

Batch job on Biowulf

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

# this file is called admix.sh

module load AdmixTools

convertf -p par.EIGENSTRAT.PED

Submit this job using the Slurm sbatch command.

sbatch admix.sh
Swarm of Jobs on Biowulf

Create a swarmfile (e.g. rolloff.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 rolloff.swarm 
Interactive job on Biowulf
Allocate an interactive node and run your job there. Sample session:
[susanc@biowulf ~]$ sinteractive
salloc.exe: Pending job allocation 17075037
salloc.exe: job 17075037 queued and waiting for resources
salloc.exe: job 17075037 has been allocated resources
salloc.exe: Granted job allocation 17075037
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1760 are ready for job

[susanc@cn1760 examples]$ module load AdmixTools
[+] Loading AdmixTools 3.0 ...

[susanc@cn1760 examples]$ rolloff -p rolloff.par

## rolloff.  Version 1002

parameter file: rolloff.par
DIR: .
indivname: example.ind
snpname: example.snp
genotypename: example.geno
poplistname: elephant.ref
admixlist: elephant.target
binsize: .001
output: Uygur
maxdis: 0.4
seed: 77
[susanc@cn1760 examples]$ exit
srun: error: cn1760: task 0: Exited with exit code 134
salloc.exe: Relinquishing job allocation 17075037
salloc.exe: Job allocation 17075037 has been revoked.
[susanc@biowulf ~]$