Flashpca on Biowulf
Quick Links
Documentation
Notes
Interactive job
Batch job
Swarm of jobs

FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data, similar to smartpca from EIGENSOFT (http://www.hsph.harvard.edu/alkes-price/software/) and shellfish (https://github.com/dandavison/shellfish). FlashPCA is based on the https://github.com/yixuan/spectra/ library.

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 flashpca

[user@cn3144 ~]$ cp /usr/local/apps/flashpca/TESTDATA/merged* .

[user@cn3144 ~]$ flashpca --bed merged.bed --fam merged.fam --bim merged.bim
[Mon Sep 24 11:57:53 2018] Start flashpca (version 2.0)
[Mon Sep 24 11:57:53 2018] seed: 1
[Mon Sep 24 11:57:53 2018] blocksize: 24766 (264699008 bytes per block)
[Mon Sep 24 11:57:53 2018] PCA begin
[Mon Sep 24 11:58:00 2018] PCA done
[Mon Sep 24 11:58:00 2018] Writing 10 eigenvalues to file eigenvalues.txt
[Mon Sep 24 11:58:00 2018] Writing 10 eigenvectors to file eigenvectors.txt
[Mon Sep 24 11:58:00 2018] Writing 10 PCs to file pcs.txt
[Mon Sep 24 11:58:00 2018] Writing 10 proportion variance explained to file pve.txt
[Mon Sep 24 11:58:00 2018] Goodbye!

[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. flashpca.sh). For example:

#!/bin/bash
set -e
module load flashpca
flashpca --bed merged.bed --fam merged.fam --bim merged.bim

Submit this job using the Slurm sbatch command.

sbatch flashpca.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. flashpca.swarm). For example:

cd folder1; flashpca --bed merged.bed --fam merged.fam --bim merged.bim
cd folder2; flashpca --bed merged.bed --fam merged.fam --bim merged.bim
cd folder3; flashpca --bed merged.bed --fam merged.fam --bim merged.bim

Submit this job using the swarm command.

swarm -f flashpca.swarm --module flashpca
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module flashpca Loads the flashpca module for each subjob in the swarm