pilon command not found

In this troubleshooting guide we learn how to fix pilon command not found error message

Introduction

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

pilon: command not found

or when using sudo you get the following error message

sudo: pilon: command not found

In Ubuntu pilon is provided by pilon package.

pilon is:

Pilon is a software tool which can be used to:

Automatically improve draft assemblies
Find variation among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:
Single base differences
Small indels
Larger indel or block substitution events
Gap filling
Identification of local misassemblies, including optional opening of new gaps

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

sudo apt-get -y install pilon

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

You can also use apt command to install pilon.

sudo apt -y install pilon

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

sudo aptitude install pilon

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