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 input.zip 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
ILLUMINACLIP:/home/andrespara/mambaforge/envs/kneadd/lib/python3.10/site-packages/kneaddata/adapters/NexteraPE-PE.fa:2:30:10
SLIDINGWINDOW:4:20 MINLEN:50
Error message returned from Trimmomatic :
java: symbol lookup error: java: undefined symbol: JLI_StringDup
This environment is using https://conda.anaconda.org/bioconda/linux-64/java-jdk-8.0.92-1.tar.bz2
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
Cheers,
A
kneadd.txt (7.8 KB)