SNP-SITES on Biowulf
SNP-sites extracts single nucleotide polymorphisms (SNPs) from a multi-FASTA alignment outputs results in multiple formats for downstream analysis.
References:
- SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, Microbial Genomics 2(4), 2016.
Documentation
Important Notes
- Module Name: snp-sites (see the modules page for more information)
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 snp-sites [+] Loading singularity 3.4.2 on cn3103 [+] Loading snp-sites 2.4.1 ... [user@cn3144 ~]$ cd /data/user/SNP-SITES_TEST [user@cn3144 ~]$ snp-sites PMEN1.aln.gz > PMEN1.out [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. snp-sites.sh). For example:
#!/bin/bash set -e module load snp-sites snp-sites /data/user/SNP-SITES_TEST/PMEN1.aln.gz > /data/user/SNP-SITES_TEST/PMEN1.out
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] TEMPLATE.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. snp-sites.swarm). For example:
snp-sites /data/user/SNP-SITES_TEST/PMEN1.aln.gz > /data/user/SNP-SITES_TEST/PMEN1.out snp-sites /data/user/SNP-SITES_TEST/ST239.aln.gz > /data/user/SNP-SITES_TEST/ST239.out
Submit this job using the swarm command.
swarm -f snp-sites.swarm [-g #] [-t #] --module snp-siteswhere
| -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 snp-sites | Loads the snp-sites module for each subjob in the swarm |