metaphlan2-data-convert command not found

In this troubleshooting guide we learn how to fix metaphlan2-data-convert command not found error message

Introduction

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

metaphlan2-data-convert: command not found

or when using sudo you get the following error message

sudo: metaphlan2-data-convert: command not found

Solutions to metaphlan2-data-convert: command not found

How To Fix metaphlan2-data-convert: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu metaphlan2-data-convert is provided by metaphlan2-data package.

metaphlan2-data is:

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0, MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.

MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the marker information file can be found at src/utils/markers_info.txt.bz2 or here) identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing:

  • unambiguous taxonomic assignments;
  • accurate estimation of organismal relative abundance;
  • species-level resolution for bacteria, archaea, eukaryotes and viruses;
  • strain identification and tracking
  • orders of magnitude speedups compared to existing methods.
  • metagenomic strain-level population genomics

This package contains the data for metaphlan2.

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

sudo apt-get -y install metaphlan2-data

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

You can also use apt command to install metaphlan2-data.

sudo apt -y install metaphlan2-data

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

sudo aptitude install metaphlan2-data

Summary

In this tutorial we learn how to fix metaphlan2-data-convert command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.