All paired-end read unmatched

Infrastructure and utilities KneadData
36

Here is the installation command based on @EacoChen’s comment, which resolved this issue in my case:
Note. I installed Trimmomatic, TRF, Bowtie2, and FastQC by myself, and the commit of KneadData I am using is 90c05f3cd25a8c74a4d804f27dd0ce52718007d8.

git clone https://github.com/biobakery/kneaddata \
    && cd kneaddata \
    && git reset --hard ebc077999b7d020f666a11aec782119ab764e00f \
    && python3 setup.py install --bypass-dependencies-install