Genome UNClutterer (GUNC) is a tool for detection of chimerism and contamination in prokaryotic genomes resulting from mis-binning of genomic contigs from unrelated lineages. It does so by applying an entropy based score on taxonomic assignment and contig location of all genes in a genome.
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 gunc [+] Loading gunc 1.0.5 on cn3144 [+] Loading singularity 4.1.5 on cn3144 [user@cn3144 ~]$ gunc -h usage: gunc [-h] [-v] ... Tool for detection of chimerism and contamination in prokaryotic genomes. options: -h, --help show this help message and exit -v, --version Print version number and exit. GUNC subcommands: run Run chimerism detection. download_db Download GUNC db. merge_checkm Merge GUNC and CheckM outputs. plot Create interactive visualisation. [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. TEMPLATE.sh). For example:
#!/bin/bash set -e module load TEMPLATE TEMPLATE < TEMPLATE.in > TEMPLATE.out
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] TEMPLATE.sh
Create a swarmfile (e.g. TEMPLATE.swarm). For example:
TEMPLATE < TEMPLATE.in > TEMPLATE.out TEMPLATE < TEMPLATE.in > TEMPLATE.out TEMPLATE < TEMPLATE.in > TEMPLATE.out TEMPLATE < TEMPLATE.in > TEMPLATE.out
Submit this job using the swarm command.
swarm -f TEMPLATE.swarm [-g #] [-t #] --module TEMPLATEwhere
-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 TEMPLATE | Loads the TEMPLATE module for each subjob in the swarm |