Trimmomatic errors

Infrastructure and utilities KneadData
1

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

2

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

3

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