High-Performance Computing at the NIH
GitHub YouTube @nih_hpc RSS Feed
Beagle on Biowulf

BEAGLE is a software program for imputing genotypes, inferring haplotype phase, and performing genetic association analysis. BEAGLE is designed to analyze large-scale data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can

Beagle was developed by Brian Browning at the University of Washington.

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@biowulf]$ sinteractive --cpus-per-task=8 --mem=8g
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 Beagle
[user@cn3144 ~]$ java -jar $BEAGLEDIR/beagle.jar nthreads=$SLURM_CPUS_PER_TASK gt=test.08Jun17.d8b.vcf.gz out=out.gt
beagle.08Jun17.d8b.jar (version 4.1)
Copyright (C) 2014-2015 Brian L. Browning
Enter "java -jar beagle.08Jun17.d8b.jar" for a summary of command line arguments.
Start time: 10:15 AM EDT on 31 Aug 2017

Command line: java -Xmx27305m -jar beagle.jar
  nthreads=8
  gt=test.08Jun17.d8b.vcf.gz
  out=out.gt

No genetic map is specified: using 1 cM = 1 Mb

reference samples:       0
target samples:        191

[ ... ]

Number of markers:                1356
Total time for building model: 6 seconds
Total time for sampling:       8 seconds
Total run time:                15 seconds

End time: 10:15 AM EDT on 31 Aug 2017
beagle.08Jun17.d8b.jar (version 4.1) finished
user@cn3144 ~]$
[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. Beagle.sh). For example:

#!/bin/bash
module load Beagle
java -jar $BEAGLEDIR/beagle.jar nthreads=$SLURM_CPUS_PER_TASK gt=test.08Jun17.d8b.vcf.gz out=out.gt

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] Beagle.sh