NGSCheckMate on Biowulf
NGSCheckMate validates nucleotide sequencing sample identity from fastq, BAM, or VCF files.
References:
- Nucleic Acids Research, Volume 45, Issue 11, 20 June 2017, Pages e103, doi:10.1093/nar/gkx193
Documentation
Important Notes
- Module Name: ngscheckmate (see the modules page for more information)
- Multithreaded/singlethreaded/MPI...
- environment variables set
- NCM_HOME
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 ~]$ ncm.py \ --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. ncm.sh). For example:
#!/bin/sh set -e module load ngscheckmate ncm.py \ --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=#] ncm.sh
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:
ncm.py -V -f -d vcf-directory1/ -O out1 -N sample1 -bed $NCM_HOME/SNP/SNP_GRCh37_hg19_woChr.bed ncm.py -V -f -d vcf-directory2/ -O out2 -N sample2 -bed $NCM_HOME/SNP/SNP_GRCh37_hg19_woChr.bed ncm.py -V -f -d vcf-directory3/ -O out3 -N sample3 -bed $NCM_HOME/SNP/SNP_GRCh37_hg19_woChr.bed ncm.py -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 ngscheckmatewhere
| -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 |