Biowulf High Performance Computing at the NIH
KING on Biowulf

KING is a toolset to explore genotype data from a genome-wide association study (GWAS) or a sequencing project. KING can be used to check family relationship and flag pedigree errors by estimating kinship coefficients and inferring IBD segments for all pairwise relationships. Unrelated pairs can be precisely separated from close relatives with no false positives, with accuracy up to 3rd- or 4th-degree (depending on array or WGS) for --related and --ibdseg analyses, and up to 2nd-degree for --kinship analysis.


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 input in bold):

[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 king

[user@cn3144 ~]$ cp $KING_EXAMPLES/* .
[user@cn3144 ~]$ king -b ex.bed --related
[user@cn3144 ~]$ king -b ex.bed --fam ex.fam --bim ex.bim --related

[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. For example:

set -e
module load king
king -b my.bed --duplicate --cpus $SLURM_CPUS_PER_TASK
king -b my.bed --related --cpus $SLURM_CPUS_PER_TASK
king -b my.bed --related --degree --cpus $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]
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. king.swarm). For example:

king -b test1.bed --fam test1.fam --bim test1.bim --related
king -b test2.bed --fam test2.fam --bim test2.bim --related
king -b test3.bed --fam test3.fam --bim test3.bim --related
king -b test4.bed --fam test4.fam --bim test4.bim --related

Submit this job using the swarm command.

swarm -f king.swarm [-g #] [-t #] --module king
-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 king Loads the king module for each subjob in the swarm