Biowulf High Performance Computing at the NIH
CAVIAR on Biowulf

CAVIAR (CAusal Variants Identication in Associated Regions), is a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants.


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 --gres lscratch:1
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 caviar
[+] Loading caviar, version a97e614...
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOBID
[user@cn3144 46116226]$ cp -r $CAVIAR_HOME/sample_data/* .
[user@cn3144 46116226]$ CAVIAR -l DDB1.top100.sig.SNPs.ld -z DDB1.top100.sig.SNPs.ZScores -o outfile
| CAVIAR!|    v2.0         |  01/Aug/2017 | 
| (C) 2017 Farhad Hormozdiari, GNU General Public License, v2 |
| For documentation, citation & bug-report instructions:      |
|            |
Max Causal=2
0 1.36408e-06
Total Likelihood= 4.552733e+48 SNP=100 

56 5.000000e-01
53 9.999984e-01

[user@cn3144 46116226]$ 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 caviar
cp -r $CAVIAR_HOME/sample_data/* .
CAVIAR -l DDB1.top100.sig.SNPs.ld -z DDB1.top100.sig.SNPs.ZScores -o outfile

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. caviar.swarm). For example:

CAVIAR -l ldfile1 -z zfile1 -o outfile1
CAVIAR -l ldfile2 -z zfile2 -o outfile2
CAVIAR -l ldfile3 -z zfile3 -o outfile3
CAVIAR -l ldfile4 -z zfile4 -o outfile4

Submit this job using the swarm command.

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