srf2fastq command not found

Introduction

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

srf2fastq: command not found

or when using sudo you get the following error message

sudo: srf2fastq: command not found

Solutions to srf2fastq: command not found

How To Fix srf2fastq: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu srf2fastq is provided by staden-io-lib-utils package.

staden-io-lib-utils is:

The io_lib from the Staden package is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows.

This package contains the programs that are distributed with the Staden io_lib for manipulating and converting sequencing data files, and in particular files to manipulate short reads generated by second and third generation sequencers and stored in SRF format.

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

sudo apt-get -y install staden-io-lib-utils

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

You can also use apt command to install staden-io-lib-utils.

sudo apt -y install staden-io-lib-utils

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

sudo aptitude install staden-io-lib-utils

Summary

In this tutorial we learn how to fix srf2fastq command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.