run_resfinder.py command not found

Introduction

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

run_resfinder.py: command not found

or when using sudo you get the following error message

sudo: run_resfinder.py: command not found

Solutions to run_resfinder.py: command not found

How To Fix run_resfinder.py: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu run_resfinder.py is provided by resfinder package.

resfinder is:

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.

ResFinder that uses BLAST for identification of acquired antimicrobial resistance genes in whole-genome data. As input, the method can use both pre-assembled, complete or partial genomes, and short sequence reads from four different sequencing platforms. The method was evaluated on 1862 GenBank files containing 1411 different resistance genes, as well as on 23 de-novo-sequenced isolates.

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

sudo apt-get -y install resfinder

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

You can also use apt command to install resfinder.

sudo apt -y install resfinder

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

sudo aptitude install resfinder

Summary

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