reportAlignmentDifferences command not found
Introduction
When you run more command in linux terminal / console, you get the following error message
reportAlignmentDifferences: command not found
or when using sudo you get the following error message
sudo: reportAlignmentDifferences: command not found
Solutions to reportAlignmentDifferences: command not found
How To Fix reportAlignmentDifferences: command not found in Ubuntu / Debian / Kali Linux / Raspbian
In Ubuntu reportAlignmentDifferences is provided by sim4db package.
sim4db is:
Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc algorithms to determine the alignments, but incorporates a fast sequence indexing and retrieval mechanism, implemented in the sister package ’leaff’, to speedily process large volumes of sequences.
While sim4db produces alignments in the same way as sim4 or sim4cc, it has additional features to make it more amenable for use with whole-genome annotation pipelines. A script file can be used to group pairings between cDNAs and their corresponding genomic regions, to be aligned as one run and using the same set of parameters. Sim4db also optionally reports more than one alignment for the same cDNA within a genomic region, as long as they meet user-defined criteria such as minimum length, percentage sequence identity or coverage. This feature is instrumental in finding all alignments of a gene family at one locus. Lastly, the output is presented either as custom sim4db alignments or as GFF3 gene features.
This package is part of the Kmer suite.
To fix this problem, we can install more using the command below.
sudo apt-get -y install sim4db
This command might take some time to finish depending on your machine internet connection.
You can also use apt command to install sim4db.
sudo apt -y install sim4db
Or if you have aptitude installed you can use the following command.
sudo aptitude install sim4db
Summary
In this tutorial we learn how to fix reportAlignmentDifferences command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.