kraken2-inspect command not found

In this troubleshooting guide we learn how to fix kraken2-inspect command not found error message

Introduction

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

kraken2-inspect: command not found

or when using sudo you get the following error message

sudo: kraken2-inspect: command not found

Solutions to kraken2-inspect: command not found

How To Fix kraken2-inspect: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu kraken2-inspect is provided by kraken2 package.

kraken2 is:

Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. [see: Kraken 1’s Webpage for more details].

Kraken 2 provides significant improvements to Kraken 1, with faster database build times, smaller database sizes, and faster classification speeds. These improvements were achieved by the following updates to the Kraken classification program:

  1. Storage of Minimizers: Instead of storing/querying entire k-mers, Kraken 2 stores minimizers (l-mers) of each k-mer. The length of each l-mer must be ≤ the k-mer length. Each k-mer is treated by Kraken 2 as if its LCA is the same as its minimizer’s LCA.
  2. Introduction of Spaced Seeds: Kraken 2 also uses spaced seeds to store and query minimizers to improve classification accuracy.
  3. Database Structure: While Kraken 1 saved an indexed and sorted list of k-mer/LCA pairs, Kraken 2 uses a compact hash table. This hash table is a probabilistic data structure that allows for faster queries and lower memory requirements. However, this data structure does have a <1% chance of returning the incorrect LCA or returning an LCA for a non-inserted minimizer. Users can compensate for this possibility by using Kraken’s confidence scoring thresholds.
  4. Protein Databases: Kraken 2 allows for databases built from amino acid sequences. When queried, Kraken 2 performs a six-frame translated search of the query sequences against the database.
  5. 16S Databases: Kraken 2 also provides support for databases not based on NCBI’s taxonomy. Currently, these include the 16S databases: Greengenes, SILVA, and RDP.

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

sudo apt-get -y install kraken2

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

You can also use apt command to install kraken2.

sudo apt -y install kraken2

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

sudo aptitude install kraken2

Summary

In this tutorial we learn how to fix kraken2-inspect command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.