parallel-fastq-dump command not found

Introduction

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

parallel-fastq-dump: command not found

or when using sudo you get the following error message

sudo: parallel-fastq-dump: command not found

Solutions to parallel-fastq-dump: command not found

How To Fix parallel-fastq-dump: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu parallel-fastq-dump is provided by parallel-fastq-dump package.

parallel-fastq-dump is:

NCBI fastq-dump can be very slow sometimes, even if you have the resources (network, IO, CPU) to go faster, even if you already downloaded the sra file. This tool speeds up the process by dividing the work into multiple threads.

This is possible because fastq-dump have options (-N and -X) to query specific ranges of the sra file, this tool works by dividing the work into the requested number of threads, running multiple fastq-dump in parallel and concatenating the results back together, as if you had just executed a plain fastq-dump call.

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

sudo apt-get -y install parallel-fastq-dump

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

You can also use apt command to install parallel-fastq-dump.

sudo apt -y install parallel-fastq-dump

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

sudo aptitude install parallel-fastq-dump

Summary

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