ERROR: Unable to find trf

I was able to get trf to run by telling kneaddata the path to trf. Try putting --trf $Path to trf in your command

trf should be in your bin folder within your environment for kneaddata. I did not have to download trf separately.

kneaddata --input1 sample.r1.fastq --input2 sample.r2.fastq -t 24 -db $MYENV/share/databases/human --trf $MYENV/bin --cat-final-output --output ./