Quick Links Batch job on Biowulf Swarm of jobs Interactive job on Biowulf

GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.

GCTA is a multithreaded application. Make sure to match the number of cpus requested with the number of threads.

Environment variables set

• $GCTAHOME: location of test data

References

• J. Yang J, S. H. Lee, M. E. Goddard and P. M. Visscher PM. GCTA: a tool for Genome-wide Complex Trait Analysis. Am J Hum Genet. 2011, 76-82. Pubmed  |  PMC  |  Journal

Documentation

• Home page

Allocate an interactive session with sinteractive and use as described above

biowulf$ sinteractive --mem=4g --cpus-per-task=2 --gres=lscratch:10
node$ module load GCTA
node$ cd /lscratch/$SLURM_JOB_ID
node$ cp $GCTAHOME/test.* .
node$ gcta --bfile test --make-grm --out test
node$ exit
biowulf$

Create a batch script similar to the following example:

#! /bin/bash
# this file is GCTA.batch
module load GCTA
gcta --bfile test --make-grm --out test

Submit to the queue with sbatch:

biowulf$ sbatch --cpus-per-task=1 --mem-per-cpus=2g GCTA.batch

Create a swarm command file similar to the following example:

# this file is GCTA.swarm
gcta --bfile test2 --make-grm --out test2
gcta --bfile test3 --make-grm --out test3
gcta --bfile test4 --make-grm --out test4

And submit to the queue with swarm

biowulf$ swarm -f GCTA.swarm --module GCTA -g 2