Fast5_to_seq_summary command not found

Introduction

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

Fast5_to_seq_summary: command not found

or when using sudo you get the following error message

sudo: Fast5_to_seq_summary: command not found

Solutions to Fast5_to_seq_summary: command not found

How To Fix Fast5_to_seq_summary: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu Fast5_to_seq_summary is provided by pycoqc package.

pycoqc is:

PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data

PycoQC relies on the sequencing_summary.txt file generated by Albacore and Guppy, but if needed it can also generates a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices and basecalled with Albacore 1.2.1+ or Guppy 2.1.3+

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

sudo apt-get -y install pycoqc

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

You can also use apt command to install pycoqc.

sudo apt -y install pycoqc

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

sudo aptitude install pycoqc

Summary

In this tutorial we learn how to fix Fast5_to_seq_summary command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.