run_gubbins command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

run_gubbins: command not found

or when using sudo you get the following error message

sudo: run_gubbins: command not found

Solutions to run_gubbins: command not found

How To Fix run_gubbins: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu run_gubbins is provided by gubbins package.

gubbins is:

Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.

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. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.

To fix this problem, we can install more using the command below.

sudo apt-get -y install gubbins

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install gubbins.

sudo apt -y install gubbins

Or if you have aptitude installed you can use the following command.

sudo aptitude install gubbins

Summary

In this tutorial we learn how to fix run_gubbins command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.