extract_markers.py command not found
Introduction
When you run more command in linux terminal / console, you get the following error message
extract_markers.py: command not found
or when using sudo you get the following error message
sudo: extract_markers.py: command not found
Solutions to extract_markers.py: command not found
How To Fix extract_markers.py: command not found in Ubuntu / Debian / Kali Linux / Raspbian
In Ubuntu extract_markers.py is provided by metaphlan2 package.
metaphlan2 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 usr/share/metaphlan2/utils/markers_info.txt.bz2) 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
To fix this problem, we can install more using the command below.
sudo apt-get -y install metaphlan2
This command might take some time to finish depending on your machine internet connection.
You can also use apt command to install metaphlan2.
sudo apt -y install metaphlan2
Or if you have aptitude installed you can use the following command.
sudo aptitude install metaphlan2
Summary
In this tutorial we learn how to fix extract_markers.py command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.