Trimmomatic errors

Hi.
I am getting an error message during the tutorial when I enter
“kneaddata --unpaired input/singleEnd.fastq --reference-db input/demo_db --output kneaddataOutputSingleEnd”

I used the same command lines as the tutorial, beginning from the install. Can you guide me on what the issue is? Thanks.

Running Trimmomatic …
CRITICAL ERROR: Error executing: java -Xmx500m -jar …bin/trimmomatic SE -threads 1 -phred33 …kneaddata_analysis/kneaddataOutputSingleEnd/reformatted_identifiersv4jo7lty_singleEnd …/kneaddata_analysis/kneaddataOutputSingleEnd/singleEnd_kneaddata.trimmed.fastq MINLEN:60 ILLUMINACLIP:…/miniconda3/envs/mpa/lib/python3.7/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:50

Error message returned from Trimmomatic :
Error: Invalid or corrupt jarfile …/miniconda3/envs/mpa/bin/trimmomatic

Hi @kogkog ,

It looks like issue with your Trimmomatic installation. Would you please try installing Trimmomatic or Kneaddata again please to see if that fixes your issue?

Regards,
Sagun

Hi Sagun

Thanks for your response. I made a new environment and installed kneaddata again, but I keep getting the same error. The version I installed is v0.12.0.

I don’t know if it can be explained, but it worked on Linux. However, I am getting errors when I use WSL2 on Windows or a Mac, even though I did the exact same thing on three different machines. Any thoughts? thank you very much for your input.

Thanks,
Taegyu