Error after collapsing to phylum level

Technical Support
1

Hello,

I am doing a meta-analysis with multiple different studies. I have a very strong study effect occurring on my data, making the PCoA plots look like "Y"s because it is so strong. Speaking with another person, they suggested that I collapse to the phylum level to remove the strong differences. However, I am encountering an error when I try to run the core-metrics after I collapse the table. Below is the example:

qiime taxa collapse
--i-table table.qza
--i-taxonomy taxonomy.qza
--p-level 2
--o-collapsed-table table-phylum.qza

qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table-phylum.qza
--p-sampling-depth 1000
--m-metadata-file metadata.txt
--output-dir core-metrics-results

The error message is as follows:
Plugin error from diversity:

All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=21): k__Bacteria;p__Cyanobacteria k__Bacteria;p__Bacteroidetes k__Bacteria;p__Planctomycetes k__Bacteria;p__Fibrobacteres k__Bacteria;p__Deferribacteres k__Bacteria;p__Verrucomicrobia k__Bacteria;p__Synergistetes k__Bacteria;__ k__Bacteria;p__OD1 k__Bacteria;p__Proteobacteria k__Bacteria;p__Tenericutes Unassigned;__ k__Bacteria;p__WPS-2 k__Bacteria;p__Fusobacteria k__Bacteria;p__Firmicutes k__Bacteria;p__Lentisphaerae k__Bacteria;p__Actinobacteria k__Bacteria;p__ k__Bacteria;p__Elusimicrobia k__Bacteria;p__Spirochaetes k__Bacteria;p__TM7

I checked the table, and I couldn't find the labels, because there was a space in-between the kingdom and phylum like this: "k__Bacteria; p__TM7" (vs this "k__Bacteria;p__TM7").

I think that might be why the error is occurring. I tried removing the spaces, but then the file was never in the correct format to use again.

Thank you,
Clinton

2

collapsing at phylum level will likely remove far too much information to yield a meaningful analysis. It sounds like you may not have study biases, per se, but unique ASVs/OTUs in each study; you may need to trim to the same lengths or, better yet, use q2-fragment-insertion (see notes and example here) to build your phylogeny and reduce some amount of this study bias (if that is not what you are doing already).

A collapsed table can no longer be used with the phylogeny because the feature IDs now consist of taxonomic labels rather than ASV/OTU IDs (which are the tip labels in the phylogeny). So you can collapse and then use non-phylogenetic methods, not not phylogenetic beta diversity methods (e.g., UniFrac).

I hope that helps!

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