# Trimmomatic errors

**URL:** <https://forum.biobakery.org/t/trimmomatic-errors/7322>\
**Category:** KneadData\
**Created:** [July 30, 2024, 2:20pm UTC](https://forum.biobakery.org/t/trimmomatic-errors/7322 "2024-07-30T14:20:39Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![kogkog](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kogkog/32/2214_2.png) [@kogkog](https://forum.biobakery.org/u/kogkog)\
**Post date:** [July 30, 2024, 2:20pm UTC](https://forum.biobakery.org/t/trimmomatic-errors/7322/1 "2024-07-30T14:20:39Z")

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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

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**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\
**Post date:** [August 2, 2024, 3:30pm UTC](https://forum.biobakery.org/t/trimmomatic-errors/7322/2 "2024-08-02T15:30:10Z")

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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

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**Author:** ![kogkog](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/kogkog/32/2214_2.png) [@kogkog](https://forum.biobakery.org/u/kogkog)\
**Post date:** [August 2, 2024, 6:25pm UTC](https://forum.biobakery.org/t/trimmomatic-errors/7322/3 "2024-08-02T18:25:15Z")

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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