run_mapsembler2_pipeline command not found
Introduction
When you run more command in linux terminal / console, you get the following error message
run_mapsembler2_pipeline: command not found
or when using sudo you get the following error message
sudo: run_mapsembler2_pipeline: command not found
Solutions to run_mapsembler2_pipeline: command not found
How To Fix run_mapsembler2_pipeline: command not found in Ubuntu / Debian / Kali Linux / Raspbian
In Ubuntu run_mapsembler2_pipeline is provided by mapsembler2 package.
mapsembler2 is:
Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters).
It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
Mapsembler2 may be used for (not limited to):
- Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced.
- Checks if a gene (input as starter) has an homolog in a set of reads
- Checks if a known enzyme is present in a metagenomic NGS read set.
- Enrich unmappable reads by extending them, possibly making them mappable
- Checks what happens at the extremities of a contig
- Remove contaminants or symbiont reads from a read set
To fix this problem, we can install more using the command below.
sudo apt-get -y install mapsembler2
This command might take some time to finish depending on your machine internet connection.
You can also use apt command to install mapsembler2.
sudo apt -y install mapsembler2
Or if you have aptitude installed you can use the following command.
sudo aptitude install mapsembler2
Summary
In this tutorial we learn how to fix run_mapsembler2_pipeline command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.