Biowulf High Performance Computing at the NIH
Phylowgs on Biowulf

A new method, PhyloWGS, can be applied to whole-genome sequencing data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations.


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:20 
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 ~]$ mkdir -p /data/$USER/phylowgs && cd /data/$USER/phylowgs

[user@cn3144 ~]$ module load phylowgs

[user@cn3144 ~]$ cp /usr/local/apps/phylowgs/TEST_DATA/* .

[user@cn3144 ~]$ ssm_data.txt cnv_data.txt -t /lscratch/$SLURM_JOBID
[2018-02-16 09:19:38.999007] Starting MCMC run...
[2018-02-16 09:19:39.004639] -1000
[2018-02-16 09:19:39.301332] Shrinking MH proposals. Now 200.000000
[2018-02-16 09:19:39.311407] -999
[2018-02-16 09:19:39.646055] Shrinking MH proposals. Now 400.000000
[2018-02-16 09:19:39.652818] -998

[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 phylowgs ssm_data.txt cnv_data.txt -t /lscratch/$SLURM_JOBID

Submit this job using the Slurm sbatch command.

sbatch --gres=lscratch:20
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. phylowgs.swarm). For example: dir1/ssm_data1.txt dir1/cnv_data1.txt -t /lscratch/$SLURM_JOBID dir2/ssm_data2.txt dir2/cnv_data2.txt -t /lscratch/$SLURM_JOBID dir3/ssm_data3.txt dir3/cnv_data3.txt -t /lscratch/$SLURM_JOBID

Submit this job using the swarm command.

swarm -f phylowgs.swarm --gres=lscratch:20 -g 5 -t 2 --module phylowgs
-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 phylowgs Loads the phylowgs module for each subjob in the swarm