bamauxmerge command not found

Introduction

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

bamauxmerge: command not found

or when using sudo you get the following error message

sudo: bamauxmerge: command not found

Solutions to bamauxmerge: command not found

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

In Ubuntu bamauxmerge is provided by biobambam2 package.

biobambam2 is:

This package contains some tools for processing BAM files, including

bamsormadup: parallel sorting and duplicate marking bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. bamsort: reads BAM and writes BAM resorted by coordinates or query name bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name

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

sudo apt-get -y install biobambam2

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

You can also use apt command to install biobambam2.

sudo apt -y install biobambam2

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

sudo aptitude install biobambam2

Summary

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