run_abundance.py command not found

Introduction

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

run_abundance.py: command not found

or when using sudo you get the following error message

sudo: run_abundance.py: command not found

Solutions to run_abundance.py: command not found

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

In Ubuntu run_abundance.py is provided by tipp package.

tipp is:

TIPP is a modification of SEPP for classifying query sequences (i.e. reads) using phylogenetic placement.

TIPP inserts each read into a taxonomic tree and uses the insertion location to identify the taxonomic lineage of the read. The novel idea behind TIPP is that rather than using the single best alignment and placement for taxonomic identification, it uses a collection of alignments and placements and considers statistical support for each alignment and placement.

TIPP can also be used for abundance estimation by computing an abundance profile on the reads binned to marker genes in a reference dataset.

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

sudo apt-get -y install tipp

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

You can also use apt command to install tipp.

sudo apt -y install tipp

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

sudo aptitude install tipp

Summary

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