Kneaddata final pair output is 0

[weichi]

Hi, this issue seems to have already been discussed in another topic.
You can try out those solutions.

All paired-end read unmatched

Here is the installation command based on @EacoChen’s comment, which can resolve this issue: git clone https://github.com/biobakery/kneaddata \ && cd kneaddata \ && git reset --hard ebc077999b7d020f666a11aec782119ab764e00f \ # the commit I use is 90c05f3cd25a8c74a4d804f27dd0ce52718007d8 && python3 setup.py install --bypass-dependencies-install

All paired-end read unmatched

If anyone is still facing this issue and doesn’t want to modify the utility.py file, you can use the following shell one-liner as a workaround. The issue arises because the following code block, which was present in version 0.10.0, is missing from the utility.py file in version 0.12.0: with open(new_file, "wt") as file_handle: for lines in read_file_n_lines(file,4): # Reformat the identifier and write to the temp file if " 1:" in lines[0]: lines[0] = lines[0].re…