hisat2_extract_snps_haplotypes_VCF.py command not found

In this troubleshooting guide we learn how to fix hisat2_extract_snps_haplotypes_VCF.py command not found error message

Introduction

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

hisat2_extract_snps_haplotypes_VCF.py: command not found

or when using sudo you get the following error message

sudo: hisat2_extract_snps_haplotypes_VCF.py: command not found

Solutions to hisat2_extract_snps_haplotypes_VCF.py: command not found

How To Fix hisat2_extract_snps_haplotypes_VCF.py: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu hisat2_extract_snps_haplotypes_VCF.py is provided by python3-hisat2 package.

python3-hisat2 is:

HISAT2 is a fast and sensitive alignment program for mapping next- generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

This package provides a serires of platform-independent scripts that are typically expected to be co-installed with the hisat2 binary.

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

sudo apt-get -y install python3-hisat2

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

You can also use apt command to install python3-hisat2.

sudo apt -y install python3-hisat2

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

sudo aptitude install python3-hisat2

Summary

In this tutorial we learn how to fix hisat2_extract_snps_haplotypes_VCF.py command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.