Hi @fstudart,
Thank you for report. What I believe is going on is that Deblur is treating _ as a special denotation character, as was done in QIIME1 for demultiplexed output, which Deblur was originally designed to process. In brief, the demultiplexed output in QIIME1 required that sequence identifiers conform to <SAMPLEID>_<INTEGER>, and the sample ID associated with the sequence was determined by splitting the sequence identifier into its sample ID and a unique integer components. My guess right now is that Deblur is not handling the per-sample files provided by QIIME2 correctly in this case, and is still assuming _ is a reserved character.
This raises two issues. First, Deblur or q2-deblur should possibly be insensitive to this, and I've opened an issue to explore it. Possibly, because previously in QIIME, _ was not allowed to be used as a character in a sample identifier, and this restriction is I believe still enforced in Qiita. What I'm wondering now is whether this reserved character should persist in QIIME2 given that there is at least one, and probably many, tools in the QIIME ecosystem which make this assumption.
@jairideout @antgonza, perhaps we should discuss on this weeks call?
Best,
Daniel