tophat-recondition.py command not found

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

Introduction

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

tophat-recondition.py: command not found

or when using sudo you get the following error message

sudo: tophat-recondition.py: command not found

Solutions to tophat-recondition.py: command not found

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

In Ubuntu tophat-recondition.py is provided by tophat-recondition package.

tophat-recondition is:

tophat-recondition is a post-processor for TopHat unmapped reads (contained in unmapped.bam), making them compatible with downstream tools (e.g., the Picard suite, samtools, GATK) (TopHat issue #17). It also works around bugs in TopHat:

  • the “mate is unmapped” SAM flag is not set on any reads in the unmapped.bam file (TopHat issue #3)
  • the mapped mate of an unmapped read can be absent from accepted_hits.bam, creating a mismatch between the file and the unmapped read’s flags (TopHat issue #16)

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

sudo apt-get -y install tophat-recondition

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

You can also use apt command to install tophat-recondition.

sudo apt -y install tophat-recondition

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

sudo aptitude install tophat-recondition

Summary

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