Kneaddata fail to recognize paired end data


I am new to kneaddata and encounter an issue in that bowtie2 does not recognize that my data are paired-end and dumps all of the reads into the “_unmatched” output files. I checked my sequence identifiers, and they look correct. Is there any suggestion to address the problem?
Besides, I’d like to know whether I can go ahead with HUMAnN microbial profiling with concatenated unmatched reads as input, considering HUMAnN uses a single input and doesn’t count paired reads.


I’m running into this problem too. I’m using the most up to date version of the kneaddata software and trying to use it for downstream analysis on metaphlan. Is it fine to use the “_unmatched” files downstream?

I tried to proceed with the concatenated unmatched data, which looks good. My understanding is that it should be fine because HUMAnN does distinguish paired-end reads.