gutSMASH is a tool that has been developed to systematically evaluate the metabolic potential of anaerobic bacteria in the gut by predicting both known and novel anaerobic metabolic gene clusters (MGCs) from the gut microbiome. The gutSMASH detection rules have been validated using a curated dataset.

References:

• Andreu, V.P., Augustijn, H.E., Chen, L., et al.Zhernakova, A., Fu, J., Fischbach, M.A., Dodd, D. and Medema, M.H. gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota. Nat Biotechnol 41, 1416–1423 (2023).

• gutSMASH Main Site
• gutSMASH on GitHub

This application requires a graphical connection using NX

• Module Name: gutsmash (see the modules page for more information)
• Multithreaded: set the -c/--cpus flag to match your allocation.
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
• Environment variables set
  • GUTSMASH_HOME
• Example files in $GUTSMASH_HOME/test
• Reference data in /fdb/gutsmash/

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task 4
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 gutsmash

[user@cn3144 ~]$ run_gutsmash.py --cpus $SLURM_CPUS_PER_TASK --minimal $GUTSMASH_HOME/test/Streptomyces_coelicolor.gbk

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

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

#!/bin/bash
set -e
module load gutsmash
run_gutsmash --cpus $SLURM_CPUS_PER_TASK --minimal $GUTSMASH_HOME/test/Streptomyces_coelicolor.gbk

Submit this job using the Slurm sbatch command.

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

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

run_gutsmash.py --cpus $SLURM_CPUS_PER_TASK --minimal sample1.gbk
run_gutsmash.py --cpus $SLURM_CPUS_PER_TASK --minimal sample2.gbk
run_gutsmash.py --cpus $SLURM_CPUS_PER_TASK --minimal sample3.gbk

Submit this job using the swarm command.

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