Hi, Thank you for the detailed log post. I think kneaddata is having a hard time tracking the read pairs. Can you check to see if the input files have “/1” and “/2” as the pair identifier at the end of each read’s sequence identifier? Also double check there are not any spaces in the sequence identifiers? I think it is likely one of these two cases that is causing kneaddata to loose track of the read’s pair id.
Thank you,
Lauren