Java error after new install

Hi all,

I am using kneaddata v0.12.0, I recently created a new environment and installed it via mamba/conda.

I just downloaded the database and I get the same error either with the data or using the custom database.

I wonder if this is due to the conda recipe or I did something wrong during the install

kneaddata --unpaired input/singleEnd.fastq --reference-db input/demo_db --output kneaddataOutputSingleEnd            
Reformatting file sequence identifiers ...

Initial number of reads ( /home/andrespara/andres/kneaddataOutputSingleEnd/reformatted_identifiers7pmlbel9_singleEnd ): 16902.0
Running Trimmomatic ... 
CRITICAL ERROR: Error executing: java -Xmx500m -jar /home/andrespara/mambaforge/envs/kneadd/bin/trimmomatic-0.33.jar 
SE -threads 1 -phred33 /home/andrespara/andres/kneaddataOutputSingleEnd/reformatted_identifiers7pmlbel9_singleEnd 
/home/andrespara/andres/kneaddataOutputSingleEnd/singleEnd_kneaddata.trimmed.fastq MINLEN:60 

Error message returned from Trimmomatic :
java: symbol lookup error: java: undefined symbol: JLI_StringDup

This environment is using

More details of the environment in the .txt attached

Thanks for your help!

Edited to add: since I managed to install in another machine I tried to install in this machine with a fixed version of java, but this didn’t work

mamba create -n kneadd -c bioconda java-jdk=7.0.91 -c biobakery kneaddata



kneadd.txt (7.8 KB)