After spent an entire day to explore our forum, I still cannot find a way to check which files were mismatched. We plan not keep same sequence in reverse and forward fastqs, but to delete those samples.
Also, I do not know why sometimes pairs of fastqs that with difference reads numbers just successfully merged, and sometimes failed.
Thank you for your attention.
The easiest way to check if the reads are matched or not is to run qiime demux summarize - the visualization will give you a good overview of what samples are present, and how many reads are in each sample (per direction).
You will need to use a newer version of QIIME 2, though - 2019.7 is quite old, I suggest upgrading to 2020.8
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