Diversity with Phylogenetic Tree


I just go through the “Moving Pictures” tutorial now.
I am mainly focused on the diversity calculation with the phylogenetic tree.
So I just download the sample dataset (rooted-tree.qza/table.qza/sample-metadata.tsv).
Using the following command line

qiime diversity core-metrics-phylogenetic
–i-phylogeny rooted-tree.qza
–i-table table.qza
–p-sampling-depth 1109
–m-metadata-file sample-metadata.tsv
–output-dir core-metrics-results

Then I get some errors.

Plugin error from diversity:

All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=35): afe1db00b504f44fb8dce4e8affc7432 06c3b8c72269d783e9d96b6e71 …

Debug info has been saved to /tmp/qiime2-q2cli-err-vd9jf23i.log

The datasets are downloaded from the QIIME website. I tried QIIME 2 2018.6 and 2018.4, but still confused about the error.
Could you please help me to solve it? Thanks!!!

Hey there @pumpkin! :jack_o_lantern:

This error means that the features (or, OTUs, if you are coming from QIIME 1) found in your feature table aren’t found in your phylogenetic tree. This means there is a data mismatch somewhere!

You could double-check that you downloaded these files from the Moving Pictures tutorial — I just searched the Moving Pictures data for a feature with the ID afe1db00b504f44fb8dce4e8affc7432 and didn’t find it — the feature table you are working with does include that feature. Maybe I misunderstood though, perhaps you are using your own data, but following MP? Let me know!

Hi @thermokarst,

Thanks for your help! I replay it. Everything goes fine if I do it step by step.
But If I just download the rooted-tree.qza, it can not work. I export the rooted-tree by QIIME and compare it with the rooted-tree.qza which is generated by the steps. They are not the same. So I was wondering if the rooted-tree.qza from QIIME website was uploaded with a mistake.
Many thanks!

Thanks for the update @pumpkin.

No, that isn’t actually even possible - the docs build the artifacts dynamically, when we create a new version of the docs.

The Phylogeny[Rooted] on the Moving Pictures tutorial 2018.6 has uuid ccc5896e-c60d-430e-a7ac-00f3dbe432af - you can confirm that the file you are using is the same file by running qiime tools peek on the qza in question, and comparing the uuid values - they should be the same.

As I mentioned above though, none of this matters if you are following with your own data (or, with changes to to the commands in the MP tutorial). For example, if you selected different trim or trunc params when running DADA2, or, if you skip DADA2 and use deblur instead. If any of that is the case for you, then this “error” makes sense — these artifacts are effectively from different studies or analyses - why would you be able to combine them in this particular way? Sounds like you are good to go now that you built a tree on your own :deciduous_tree:

Have fun! :qiime2:

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