Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.

References:

• Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R. Nucleic Acids Research, Volume 43, Issue 3, 18 February 2015, Page e15.

• Gubbins Main Site

• Module Name: gubbins (see the modules page for more information)

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 gubbins
[+] Loading singularity  3.4.2  on cn3144 
[+] Loading gubbins 2.3.4  ... 

[user@cn3144 ~]$ cd /data/user/GUBBINS_TEST

[user@cn3144 ~]$ ls
PMEN1.aln.gz  ST239.aln.gz

[user@cn3144 ~]$ gunzip PMEN1.aln.gz

[user@cn3144 ~]$ gunzip ST239.aln.gz

[user@cn3144 ~]$ ls
PMEN1.aln  ST239.aln

[user@cn3144 ~]$ gubbins PMEN1.aln

[user@cn3144 ~]$ ls PMEN1.*
PMEN1.aln				PMEN1.filtered_polymorphic_sites.phylip  PMEN1.recombination_predictions.embl
PMEN1.aln.seq.joint.txt			PMEN1.final_tree.tre			 PMEN1.recombination_predictions.gff
PMEN1.branch_base_reconstruction.embl	PMEN1.node_labelled.final_tree.tre	 PMEN1.summary_of_snp_distribution.vcf
PMEN1.filtered_polymorphic_sites.fasta	PMEN1.per_branch_statistics.csv

[user@cn3144 ~]$ gubbins ST239.aln

[user@cn3144 ~]$ ls ST239.*
ST239.aln				ST239.filtered_polymorphic_sites.phylip  ST239.recombination_predictions.embl
ST239.aln.seq.joint.txt			ST239.final_tree.tre			 ST239.recombination_predictions.gff
ST239.branch_base_reconstruction.embl	ST239.node_labelled.final_tree.tre	 ST239.summary_of_snp_distribution.vcf
ST239.filtered_polymorphic_sites.fasta	ST239.per_branch_statistics.csv

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. gubbins.sh). For example:

#!/bin/bash
set -e
module load gubbins
cd /data/user/GUBBINS_TEST
gubbins PMEN1.aln

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] gubbins.sh

Create a swarmfile (e.g. gubbins.swarm). For example:

cd /data/user/GUBBINS_TEST; gubbins PMEN1.aln
cd /data/user/GUBBINS_TEST; gubbins ST239.aln

Submit this job using the swarm command.

swarm -f gubbins.swarm [-g #] [-t #] --module gubbins