ea-alc command not found

In this troubleshooting guide we learn how to fix ea-alc command not found error message

Introduction

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

ea-alc: command not found

or when using sudo you get the following error message

sudo: ea-alc: command not found

Solutions to ea-alc: command not found

How To Fix ea-alc: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu ea-alc is provided by ea-utils package.

ea-utils is:

Ea-utils provides a set of command-line tools for processing biological sequencing data, barcode demultiplexing, adapter trimming, etc.

Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

Main Tools are:

  • fastq-mcf Scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set of clipping parameters and performs clipping. Also does skewing detection and quality filtering.
  • fastq-multx Demultiplexes a fastq. Capable of auto-determining barcode id’s based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they’re not.
  • fastq-join Similar to audy’s stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It uses the same “squared distance for anchored alignment” as other tools.
  • varcall Takes a pileup and calculates variants in a more easily parameterized manner than some other tools.

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

sudo apt-get -y install ea-utils

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

You can also use apt command to install ea-utils.

sudo apt -y install ea-utils

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

sudo aptitude install ea-utils

Summary

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