Biowulf High Performance Computing at the NIH
SURVIVOR on Biowulf

SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.


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 survivor

[user@cn3144 ~]$ ls *vcf > sample-files
[user@cn3144 ~]$ SURVIVOR merge sample-files 1000 2 1 1 0 30 sample-merged.vcf

[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 survivor
SURVIVOR bincov lowMQ.cov 10 2 > lowMQ.bed

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. survivor.swarm). For example:

SURVIVOR merge sample1-files 1000 2 1 1 0 30 sample1-merged.vcf
SURVIVOR merge sample2-files 1000 2 1 1 0 30 sample2-merged.vcf
SURVIVOR merge sample3-files 1000 2 1 1 0 30 sample3-merged.vcf
SURVIVOR merge sample4-files 1000 2 1 1 0 30 sample4-merged.vcf

Submit this job using the swarm command.

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