running dada2 followed by beta-phylogenetic

Hi,

I wanted to run dada2 on simulated reads (produced using grinder) to obtain the feature table and run beta-phylogenetic after, using the feature table produced by dada2. Is this possible? I was able to get the feature table. However, when I was trying to run beta-phylogenetic, I received an error "The table does not appear to be completely represented by the phylogeny.". I'm very sure the read data had the same id as those on the phylogenetic tree. Could it be the formatting after dada2 that made it unrecognizable? I'm not sure how to debug. Found posts having similar issues, but don't think they can apply.
Attaching the data below (attached the original tree before imported):
qiimeinput.zip (989.5 KB) 99_otus.tree (4.9 MB)
Here are the commands:

qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path manifest.txt --output-path demux.qza --input-format SingleEndFastqManifestPhred33
Dada2: qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-trunc-len 0 --p-n-threads 10 --output-dir qiimeoutput
qiime diversity beta-phylogenetic --i-table table.qza --i-phylogeny 99_otu_tree.qza --p-metric weighted_unifrac --o-distance-matrix dmatrix.qza
Any help is appreciated. Thank you!

Hi @wei_wei, welcome to :qiime2: !

The error is due to the fact that the IDs of your ASVs (features) output from DADA2, do not match the IDs in the given tree. Ideally, the tree should have been made with your own ASVs, either using a de novo or fragment-insertion approach.

It appears you are trying to use the pre-computed GreenGenes tree?

I recommend reading through the Phylogenetic Inference tutorial, on how to make a tree based on your sequence data.

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Hi Mike,

Thank you so much for your reply! Yes I was trying to use the pre-computed GreenGenes tree. Just wondering, is it possible to use the pre-computed tree? The read data before dada2 have IDs matching the pre-computed GreenGenes tree. How different will the inferred tree be from the pre-computed tree?
Thank you!

Yes. Again, read through the tutorial I linked above and read about the fragment insertion method. Just use the precomputed sepp files.

You can also follow along with the fragment-insertion portion of the PD mouse tutorial, to get an idea of how this process works.

Finally, check out the following related videos on YouTube:

If you are interested in a better way to visualize your phylogenies within :qiime2: also, checkout Empress.

-Cheers!

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