Biowulf High Performance Computing at the NIH
GEMMA on Biowulf & Helix

GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS):

GEMMA was developed in the Zhou Lab at U. Michigan. GEMMA website.

Documentation and 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 57710203
salloc.exe: job 57710203 queued and waiting for resources
salloc.exe: job 57710203 has been allocated resources
salloc.exe: Granted job allocation 57710203
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3115 are ready for job

[user@cn3115 ~]$ mkdir -p /scratch/$USER/gemma-test

[user@cn3115 ~]$ cd /scratch/$USER/gemma-test

[user@cn3115 ~]$ module load GEMMA
[+] Loading GEMMA 0.98.1  ...

[user@cn3115 ~]$ gemma -g $GEMMA_EXAMPLES/mouse_hs1940.geno.txt.gz -p $GEMMA_EXAMPLES/mouse_hs1940.pheno.txt -gk -o mouse_hs1940
GEMMA 0.98.1 (2018-12-10) by Xiang Zhou and team (C) 2012-2018
Reading Files ...
## number of total individuals = 1940
## number of analyzed individuals = 1410
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs/var        =    12226
## number of analyzed SNPs         =    10768
Calculating Relatedness Matrix ...
================================================== 100%
**** INFO: Done.

[user@cn3115 ~]$ exit
exit
salloc.exe: Relinquishing job allocation 57710203
salloc.exe: Job allocation 57710203 has been revoked.

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. gemma.sh). For example, to run the threaded version of hyphy:

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

module load GEMMA
mkdir -p /scratch/$USER/gemma-test
cd /scratch/$USER/gemma-test

gemma -g $GEMMA_EXAMPLES/mouse_hs1940.geno.txt.gz \
      -p $GEMMA_EXAMPLES/mouse_hs1940.pheno.txt \
      -gk -o mouse_hs1940

Submit this job using the Slurm sbatch command.

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