I don't find trimmomatic.jar file

Question

[Hayler Edu]

Hello everyone.

I installed trimmomatic on my computer using conda. The problem is that when I try to execute trimmomatic I have an error because I don't have a file with the name "trimmomatic-036.jar"

This is the command that I'm trying to execute

java -jar /home/linuxngs/Escritorio/NGS/Trimmomatic-0.36/trimmomatic-0.36.jar PE -threads 20 -phred33 -trimlog logFile /home/linuxngs/Escritorio/Datos/SEC1_chr10.1.fastq

[Arup Ghosh]

Try just trimmomatic/Trimmomatic after activating the conda environment.

[Ambu Vijayan]

What is the name of the conda environment that you used to create? Hopefully you used this command to install trimmomatic -> conda install -c bioconda trimmomatic Use command -> conda env list Lets assume the name is trimmomatic Then the command to activate the conda environment is -> conda activate trimmomatic

Then to run trimmomatic just use this command accordingly :

trimmomatic PE -threads 4 SRR_1056_1.fastq SRR_1056_2.fastq \ SRR_1056_1.trimmed.fastq SRR_1056_1un.trimmed.fastq \ SRR_1056_2.trimmed.fastq SRR_1056_2un.trimmed.fastq \ ILLUMINACLIP:adapters.fa SLIDINGWINDOW:4:20

trimmomatic SE -threads 4 SRR_1056.fastq \ SRR_1056.trimmed.fastq SRR_1056_un.trimmed.fastq \ ILLUMINACLIP:SRR_adapters.fa SLIDINGWINDOW:4:20

[Hayler Edu]

Helloooo thank you for the help to resolve the error

Answer 1

[Prosad]

Hi,

The problem is that you have installed trimmomatic from conda and you are trying to run it from a local file location (/home/linuxngs/Escritorio/NGS/Trimmomatic-0.36/trimmomatic-0.36.jar), probably it is not there because you have not downloaded as a jar file and this is the reason it is showing the error.

You have to run it within the conda environment.

First make sure you have trimmomatic installed in your current conda environment by typing:

conda list | grep "trimmomatic"

If it is installed then above command will show which version is installed.

Then it is pretty straightforward, you have to type

trimmomatic PE -threads 20 -phred33 -trimlog logFile /home/linuxngs/Escritorio/Datos/SEC1_chr10.1.fastq

and please make sure you're using paired end reads. You are using "PE" and using only a single input file.

hope it helps!