I am trying to decontaminate the sequencing run (SRR9680494). I still get 66% human reads left. Is there something wrong with the command I am using?
kneaddata --remove-intermediate-output -t 2 --input split_1.fastq --input split_2.fastq --output clean --reference-db /opt/data/decontamination/GRCh38_phix.index --bowtie2-options “–very-sensitive --dovetail” --trimmomatic-options “SLIDINGWINDOW:4:20 MINLEN:50”