Qiime demux: Consider adding warning if missing samples and sequence count low

I realized I forgot to add the reverse compliment parameters to my qiime demux... command. This was an oversight because this time I wasn’t the one who barcoded and prepped these samples so I just didn’t have it on my mind.

I noticed that it runs with no errors, but obviously the code was looking for the wrong sequence so it makes sense I was missing most of my samples and had sequence counts of about 1 or 2. If I hadn’t previously done these analyses, I probably would have really panicked. With sequence counts of below a certain threshold and with so many missing samples, the user could be given a Qiime warning to consider using reverse compliment. Just a thought because I could see this being a stressor for users especially in such an important early step. Just an idea.

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I’ve definitely seen a lot of people run into this problem, although usually it’s because they added the rev-comp param when they didn’t need to!

I think a technical challenge would be emitting a warning, as right now q2cli captures stdout and stderr by default, so if you weren’t looking for the warning, you wouldn’t necessarily see it… I’m sure there’s something we could emit and capture between the framework and the interfaces though!

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One option would be to add a warning box in the demux summarize visualization. Viewing that is when people typically realize that they have this problem, so we could put an info box in there if the count is very low to note that the user may need to toggle their rev-comp parameter.