Biowulf High Performance Computing at the NIH
NGSCheckMate on Biowulf

NGSCheckMate validates nucleotide sequencing sample identity from fastq, BAM, or VCF files.


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
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 ngscheckmate
[-] Unloading ngscheckmate, version 1.0.0...
[-] Unloading samtools 1.6 ...
[+] Loading samtools 1.6 ...
[+] Loading gcc 7.2.0 ...
[+] Loading ngscheckmate, version 1.0.0...
[user@cn3144 ~]$ \
--VCF \
--family-cutoff \
--dir vcf-directory/ \
--outdir output-dir/ \
--outfilename sample \
-bed $NCM_HOME/SNP/SNP_GRCh37_hg19_woChr.bed

[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 ngscheckmate \
 --VCF \
 --family-cutoff \
 --dir vcf-directory/ \
 --outdir output-dir/ \
 --outfilename sample \
 -bed $NCM_HOME/SNP/SNP_GRCh37_hg19_woChr.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. TEMPLATE.swarm). For example: -V -f -d vcf-directory1/ -O out1 -N sample1 -bed $NCM_HOME/SNP/SNP_GRCh37_hg19_woChr.bed -V -f -d vcf-directory2/ -O out2 -N sample2 -bed $NCM_HOME/SNP/SNP_GRCh37_hg19_woChr.bed -V -f -d vcf-directory3/ -O out3 -N sample3 -bed $NCM_HOME/SNP/SNP_GRCh37_hg19_woChr.bed -V -f -d vcf-directory4/ -O out4 -N sample4 -bed $NCM_HOME/SNP/SNP_GRCh37_hg19_woChr.bed

Submit this job using the swarm command.

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