TransDecoder.Predict command not found
Introduction
When you run more command in linux terminal / console, you get the following error message
TransDecoder.Predict: command not found
or when using sudo you get the following error message
sudo: TransDecoder.Predict: command not found
Solutions to TransDecoder.Predict: command not found
How To Fix TransDecoder.Predict: command not found in Ubuntu / Debian / Kali Linux / Raspbian
In Ubuntu TransDecoder.Predict is provided by transdecoder package.
transdecoder is:
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
TransDecoder identifies likely coding sequences based on the following criteria:
- a minimum length open reading frame (ORF) is found in a transcript sequence
- a log-likelihood score similar to what is computed by the GeneID software is > 0.
- the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames.
- if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc).
- optional the putative peptide has a match to a Pfam domain above the noise cutoff score.
To fix this problem, we can install more using the command below.
sudo apt-get -y install transdecoder
This command might take some time to finish depending on your machine internet connection.
You can also use apt command to install transdecoder.
sudo apt -y install transdecoder
Or if you have aptitude installed you can use the following command.
sudo aptitude install transdecoder
Summary
In this tutorial we learn how to fix TransDecoder.Predict command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.