haarz command not found

Introduction

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

haarz: command not found

or when using sudo you get the following error message

sudo: haarz: command not found

Solutions to haarz: command not found

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

In Ubuntu haarz is provided by segemehl package.

segemehl is:

Segemehl is a software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl accepts fasta and fastq queries (gzip’ed and bgzip’ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file. In the case of split-read mapping, additional BED files are written to the disc. These BED files may be summarized with the postprocessing tool haarz. In the case of the alignment of bisulfite converted reads, raw methylation rates may also be called with haarz.

In brief, for each suffix of a read, segemehl aims to find the best-scoring seed. Seeds might contain insertions, deletions, and mismatches (differences). The number of differences allowed within a single seed is user-controlled and is crucial for the runtime of the program. Subsequently, seeds that undercut the user-defined E-value are passed on to an exact semi-global alignment procedure. Finally, reads with a minimum accuracy of percent are reported to the user.

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

sudo apt-get -y install segemehl

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

You can also use apt command to install segemehl.

sudo apt -y install segemehl

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

sudo aptitude install segemehl

Summary

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