Emperor files showing black screen

[rob-ferg]

Hello,

I ran a test with 3 sample files, which completed with no reported errors. I am able to view most of the results, except for the Emperor diversity plots. Whenever I try to view them on QIIME 2 view, it only shows a black screen, and when I try to select SampleID or condition in the legend, it only shows 2 of the 3 sample/condition names. I'll upload an image under this message.
Also, I am only able to view one phylogenetic tree on the .nwk files -- I expected to be able to generate a phylogenetic tree for each condition.
I tried re-running the pipeline, but ended up with the same two issues.
Any guidance would be greatly appreciated.

Thanks,
Robbie

[proteinosome]

Re: View issue, I'm not sure and I have not seen it before. Please check whether there's anything strange with the pipeline results (e.g. are you getting ASVs at all and are they classified correctly?). If it's a view issue I'd suggest reaching out to the QIIME developers.

Re: Phylogenetic tree, right now the pipeline outputs a simplistic tree using all ASVs from all samples. You will have to write your own script to generate one tree per condition if desired. The output of the pipeline should be compatible with QIIME tools so it should be pretty straightforward to do it.