Biowulf High Performance Computing at the NIH
PAINTOR on Biowulf

PAINTOR is a statistical fine-mapping method that integrates functional genomic data with association strength from potentially multiple populations (or traits) to prioritize variants for follow-up analysis. The software runs on multiple fine-mapping loci and/or populations/traits simultaneously and takes as input the following data for each set of SNPs at a locus


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 PAINTOR

[user@cn3144 ~]$ cp -pr /usr/local/apps/PAINTOR/SampleData  /data/$USER 

[user@cn3144 ~]$ cd /data/$USER

[user@cn3144 ~]$ PAINTOR -input SampleData/input.files    -in SampleData/  \
      -out SampleData/    -Zhead Zscore -LDname ld    -enumerate 2   -annotations DHS
Running PAINTOR with full enumeration
Maximum number of causals per locus: 2
Proportion of LD variance kept when performing truncated SVD for estimating N*h2g: 0.95
Model annotations: DHS
Reading in files for: Locus1
Enrichment estimates at iteration 11 is :
Average log bayes factor: 658.648

[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 PAINTOR
cp -pr /usr/local/apps/PAINTOR/SampleData  /data/$USER
PAINTOR -input SampleData/input.files    -in SampleData/  \
      -out SampleData/    -Zhead Zscore -LDname ld    -enumerate 2   -annotations DHS

Submit this job using the Slurm sbatch command.

sbatch [--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. PAINTOR.swarm). For example:

PAINTOR -input dir1/input.files    -in dir1/  -out dir1  -Zhead Zscore -LDname ld  -enumerate 2 -annotations DHS
PAINTOR -input dir2/input.files    -in dir2/  -out dir1  -Zhead Zscore -LDname ld  -enumerate 2 -annotations DHS
PAINTOR -input dir3/input.files    -in dir3/  -out dir1  -Zhead Zscore -LDname ld  -enumerate 2 -annotations DHS

Submit this job using the swarm command.

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