get_species_taxids command not found

Introduction

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

get_species_taxids: command not found

or when using sudo you get the following error message

sudo: get_species_taxids: command not found

Solutions to get_species_taxids: command not found

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

In Ubuntu get_species_taxids is provided by ncbi-blast+ package.

ncbi-blast+ is:

The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM’s. The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service.

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

sudo apt-get -y install ncbi-blast+

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

You can also use apt command to install ncbi-blast+.

sudo apt -y install ncbi-blast+

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

sudo aptitude install ncbi-blast+

Summary

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