hits_to_fastq command not found

Introduction

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

hits_to_fastq: command not found

or when using sudo you get the following error message

sudo: hits_to_fastq: command not found

Solutions to hits_to_fastq: command not found

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

In Ubuntu hits_to_fastq is provided by seer package.

seer is:

Bacterial genomes vary extensively in terms of both gene content and gene sequence - this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. SEER provides a computationally scalable and widely applicable statistical method for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable- length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogen Streptococcus pneumoniae, SEER identifies relevant previously characterised resistance determinants for several antibiotics.

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

sudo apt-get -y install seer

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

You can also use apt command to install seer.

sudo apt -y install seer

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

sudo aptitude install seer

Summary

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