faidx command not found

Introduction

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

faidx: command not found

or when using sudo you get the following error message

sudo: faidx: command not found

Solutions to faidx: command not found

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

In Ubuntu faidx is provided by python3-pyfaidx package.

python3-pyfaidx is:

Samtools provides a function “faidx” (FAsta InDeX), which creates a small flat index file “.fai” allowing for fast random access to any subsequence in the indexed FASTA file, while loading a minimal amount of the file in to memory. This Python module implements pure Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index. The pyfaidx module is API compatible with the pygr seqdb module. A command-line script “faidx” is installed alongside the pyfaidx module, and facilitates complex manipulation of FASTA files without any programming knowledge.

This package provides the Python 3 modules to access fasta files.

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

sudo apt-get -y install python3-pyfaidx

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

You can also use apt command to install python3-pyfaidx.

sudo apt -y install python3-pyfaidx

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

sudo aptitude install python3-pyfaidx

Summary

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