gsnapl.avx2 command not found

In this troubleshooting guide we learn how to fix gsnapl.avx2 command not found error message

Introduction

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

gsnapl.avx2: command not found

or when using sudo you get the following error message

sudo: gsnapl.avx2: command not found

Solutions to gsnapl.avx2: command not found

How To Fix gsnapl.avx2: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu gsnapl.avx2 is provided by gmap package.

gmap is:

This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of

known splice sites and identify novel splice sites.
known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA.

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

sudo apt-get -y install gmap

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

You can also use apt command to install gmap.

sudo apt -y install gmap

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

sudo aptitude install gmap

Summary

In this tutorial we learn how to fix gsnapl.avx2 command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.