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