Eigensoft on HPC
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Documentation
Notes
Interactive job
Batch job
Swarm of jobs

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Note, the programs eigenstrat and eigenstratQTL of EIGENSOFT version 2.0
have been replaced by smarteigenstrat.perl. Please refer to documentation.
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The EIGENSOFT package combines functionality from population genetics methods (Patterson et al. 2006) and EIGENSTRAT stratification correction me thod (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axe s of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.Eigensoft was developed at Harvard Genetics Department and the Broad Institute.

 

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
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 eigensoft

[user@cn3144 ~]$ cp -rp /usr/local/apps/eigensoft/6.1.4/CONVERTF /data/$USER
[user@cn3144 ~]$ cd /data/$USER/CONVERTF
[user@cn3144 ~]$ perl example.perl
[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. batch.sh). For example:

#!/bin/bash
set -e
module load eigensoft
eigensoft commands

Submit this job using the Slurm sbatch command.

sbatch batch.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. job.swarm). For example:

cd dir1; eigensoft commands
cd dir2; egiensoft commands
cd dir3; eigensoft commands

Submit this job using the swarm command.

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