Diversity plug-in error

[Nicholas_Bokulich]

Hi @LauraMason,

@LauraMason

However, when I look at the OTU table summary in Qiime1, it looks like I have only 7 samples. I’m really not sure what is going on with this.

This is all sounding really fishy — it sounds like something may have gone wrong in qiime1, which is unsupported at this point so it makes diagnosing this issue a bit convoluted and difficult. Whenever I find myself in a position like this, I always feel that it is easier to wipe the slate and start over, rather than retrace my steps!

@LauraMason

As far as importing raw sequences into Qiime2, I am working with 454 data, and I thought the OTU (ASV?) picking algorithm was Illumina specific? Or is this where I would use vsearch as my OTU picking method?

You are correct, dada2 is specific for Illumina — 454 support is forthcoming. You should use vsearch for OTU picking.

@LauraMason

I tried that, ran into an error, and figured it was just easiest to use Qiime1 up until the biom table step & import it. What do you recommend?

Helping you debug a q2-vsearch error would probably be a lot easier than trying to debug your current error, now that it sounds like the issues might stretch all the way back to qiime1. (if you go that route, please open a new forum thread so it's easier for other users to search )

Were you able to import your 454 reads into QIIME2? I recall that you had issues with importing and I just want to make sure the vsearch error was not related to that.

@LauraMason

OTU picking method (qiime1):

pick_otus.py -i seqs.fna -o seqs_otus -m usearch61 -s 0.97

Oh wow, that takes me back . You're doing things the old school way — one of the OTU picking workflows in qiime1 like pick_open_reference_otus.py would save you some of the legwork (all of q2-vsearch's methods are similar workflows so that you don't need to manually convert OTU maps to feature tables). And might be the cause of this issue, as I noted above if you are building your OTU table off of the wrong OTU map.

So my personal preference is to do it all in QIIME2 and support would be easier — but I suppose that depends on the vsearch error you are having. If you cannot import your 454 data into QIIME2 to begin with, that changes matters...