fix-trinity-output command not found

Introduction

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

fix-trinity-output: command not found

or when using sudo you get the following error message

sudo: fix-trinity-output: command not found

Solutions to fix-trinity-output: command not found

How To Fix fix-trinity-output: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu fix-trinity-output is provided by ruby-fix-trinity-output package.

ruby-fix-trinity-output is:

trinityrnaseq outputs fastq files that have been ‘corrected’

Unfortunately these files are no longer properly paired and therefore can’t be used in most aligners such as bowtie2 and snap-aligner. This script attempts to fix that and produce 2 properly paired fastq files and a fastq file containing single reads

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

sudo apt-get -y install ruby-fix-trinity-output

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

You can also use apt command to install ruby-fix-trinity-output.

sudo apt -y install ruby-fix-trinity-output

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

sudo aptitude install ruby-fix-trinity-output

Summary

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