Hi @anndonxlow and @Mike_Stevenson ,
I don't think the file extension is the problem here. demux.qz.qza has .qza extension, regardless of whether there are more points (.) before the final one.¹ Moreover, the error message shows that DADA2 is indeed working until the chimera removal step.
We addressed this error recently in the forum. In my first reply of this post I put some links to similar questions, and I outline two possible reasons for this error to happen. Long story short, it is quite likely that either:
- Your paired-end reads are not merging due to too aggressive filtering parameters.
- You are using the same reads as forward and reverse.
Best,
Sergio
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¹ If you are curious about this, you can read some on why file extensions are not that important here.