run_dada_single.R command not found

In this troubleshooting guide we learn how to fix run_dada_single.R command not found error message

Introduction

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

run_dada_single.R: command not found

or when using sudo you get the following error message

sudo: run_dada_single.R: command not found

Solutions to run_dada_single.R: command not found

How To Fix run_dada_single.R: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu run_dada_single.R is provided by q2-dada2 package.

q2-dada2 is:

QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features:

  • Integrated and automatic tracking of data provenance
  • Semantic type system
  • Plugin system for extending microbiome analysis functionality
  • Support for multiple types of user interfaces (e.g. API, command line, graphical)

QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline.

QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed.

This package wraps the dada2 R package in BioConductor for modeling and correcting Illumina-sequenced amplicon errors. This was shown to improve the sensitivity of diversity analyses.

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

sudo apt-get -y install q2-dada2

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

You can also use apt command to install q2-dada2.

sudo apt -y install q2-dada2

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

sudo aptitude install q2-dada2

Summary

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