Empty paired files

[weichi]

It might help.

All paired-end read unmatched

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

Alternatively, try installing the latest version, which is v0.12.1.