indexdb_rna command not found

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

Introduction

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

indexdb_rna: command not found

or when using sudo you get the following error message

sudo: indexdb_rna: command not found

Solutions to indexdb_rna: command not found

How To Fix indexdb_rna: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu indexdb_rna is provided by sortmerna package.

sortmerna is:

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. Additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1). SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user. Optionally, it can provide high quality local alignments of rRNA reads against the rRNA database. SortMeRNA works with Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.

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

sudo apt-get -y install sortmerna

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

You can also use apt command to install sortmerna.

sudo apt -y install sortmerna

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

sudo aptitude install sortmerna

Summary

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