pairtools command not found

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

Introduction

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

pairtools: command not found

or when using sudo you get the following error message

sudo: pairtools: command not found

In Ubuntu pairtools is provided by python3-pairtools package.

python3-pairtools is:

Simple and fast command-line framework to process sequencing data from a Hi-C experiment.

Process pair-end sequence alignments and perform the following operations:

Detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end sequences of Hi-C DNA molecules
Sort .pairs files for downstream analyses
Detect, tag and remove PCR/optical duplicates
Generate extensive statistics of Hi-C datasets
Select Hi-C pairs given flexibly defined criteria
Restore .sam alignments from Hi-C pairs

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

sudo apt-get -y install python3-pairtools

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

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

sudo apt -y install python3-pairtools

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

sudo aptitude install python3-pairtools

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