polish_clusters command not found

In this troubleshooting guide we learn how to fix polish_clusters command not found error message

Introduction

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

polish_clusters: command not found

or when using sudo you get the following error message

sudo: polish_clusters: command not found

In Ubuntu polish_clusters is provided by pinfish package.

pinfish is:

The toolchain is composed of the following tools:

spliced_bam2gff - a tool for converting sorted BAM files containing spliced alignments into GFF2 format. Each read will be represented as a distinct transcript. This tool comes handy when visualizing spliced reads at particular loci and to provide input to the rest of the toolchain.
cluster_gff - this tool takes a sorted GFF2 file as input and clusters together reads having similar exon/intron structure and creates a rough consensus of the clusters by taking the median of exon boundaries from all transcripts in the cluster.
polish_clusters - this tool takes the cluster definitions generated by cluster_gff and for each cluster creates an error corrected read by mapping all reads on the read with the median length and polishing it using racon. The polished reads can be mapped to the genome using minimap2 or GMAP.
collapse_partials - this tool takes GFFs generated by either cluster_gff or polish_clusters and filters out transcripts which are likely to be based on RNA degradation products from the 5’ end. The tool clusters the input transcripts into “loci” by the 3’ ends and discards transcripts which have a compatible transcripts in the loci with more exons.

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

sudo apt-get -y install pinfish

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

You can also use apt command to install pinfish.

sudo apt -y install pinfish

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

sudo aptitude install pinfish

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