racon_wrapper.py command not found

Introduction

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

racon_wrapper.py: command not found

or when using sudo you get the following error message

sudo: racon_wrapper.py: command not found

Solutions to racon_wrapper.py: command not found

How To Fix racon_wrapper.py: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu racon_wrapper.py is provided by racon package.

racon is:

Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.

Racon can be used as a polishing tool after the assembly with either Illumina data or data produced by third generation of sequencing. The type of data inputed is automatically detected.

Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files can be compressed with gzip.

Racon can also be used as a read error-correction tool. In this scenario, the MHAP/PAF/SAM file needs to contain pairwise overlaps between reads including dual overlaps.

A wrapper script is also available to enable easier usage to the end- user for large datasets. It has the same interface as racon but adds two additional features from the outside. Sequences can be subsampled to decrease the total execution time (accuracy might be lower) while target sequences can be split into smaller chunks and run sequentially to decrease memory consumption. Both features can be run at the same time as well.

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

sudo apt-get -y install racon

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

You can also use apt command to install racon.

sudo apt -y install racon

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

sudo aptitude install racon

Summary

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