Plugin error from Diversity

I’m trying to run alpha and beta diversity analyses with data I’ve downloaded from Qiita and
I’m receiving a pluggin error. I converted qiime artifacts into .qza files following this tutorial. I’m running QIIME2 version 2018.11 and installed it using conda.
Here is the command I’m trying to run:

qiime diversity core-metrics-phylogenetic
–i-phylogeny rooted-tree.qza
–i-table table.qza
–p-sampling-depth 12476
–m-metadata-file sample-metadata.tsv
–output-dir core-metrics-results

Here is the error I received:

Plugin error from diversity:

All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=93):

I’m a beginner, so any advice/explanation on what this error is and how it generally occurs would be appreciated.

rooted-tree.qza (2.5 MB)

table.qza (547.3 KB)

sample-metadata.txt (1.4 MB)

rep-seqs.qza (181.1 KB)

Hi Vivianna_Sanchez,

This error means that the samples that are present in your biom table are not all located on your phylogenetic tree. Can you tell me where you got your table.qza from (is it from closed reference OTU table, deblur reference hit table, or deblur final hit table) and which rooted-tree.qza you’re using (if it’s from the closed reference OTU table is it: greengenes, SILVA, UNITE or is it from the deblur reference hit table)?




Hello Stephanie,

Both my table.qza file and rooted-tre.qza are from a deblur reference hit table.


Hi Vivianna,

So you will have to filter your table.qza based on your tree.qza (basically removing any OTUs that aren’t present on your tree). There are 3 ways to do this.

  1. Run the qiime fragment-insertion filter-features that will filter your table.qza to only contain the OTUs found in your tree.

  2. On Qiita, go to create analysis and create an analysis using your deblur reference hit table. Download the biom table from your first analysis artifact instead of the one located on the deblur reference table on the study page. When you create an analysis from the deblur reference-hit table, it automatically removes the OTUs that are not located on the phylogenetic tree so you don’t have to do it.

  3. You can follow the steps listed in the tutorial you referred to that were written prior to the qiime fragment-insertion filter-feature command being included in the core QIIME2 commands. Run the following commands:

echo “feature-id” > qiita-files/sepp-tips.txt

python -c “from skbio.tree import TreeNode; print(’\n’.join([
for tip in‘qiita-files/insertion_tree.relabelled.fix.tre’).tips()
if not]))” >> qiita-files/sepp-tips.txt

qiime feature-table filter-features
–i-table qiita-files/feature-table.qza
–m-metadata-file qiita-files/sepp-tips.txt
–o-filtered-table feature-table.qza



This solved my problem, thank you!

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.