Plugin error from diversity: table does not appear to be completely represented by the phylogeny.

Hello. I am trying to do alpha and beta diversity analyses with AGP (American Gut Project) data and am getting the error shown below the second chunk of code shown below. data.qza is a feature table which is deblurred sequences downloaded from redbiom.

Any help would be greatly appreciated! Thank you :slight_smile:

qiime phylogeny align-to-tree-mafft-fasttree \

–i-sequences data_rep_seqs.qza
–p-parttree
–o-alignment aligned-rep-seqs.qza
–o-masked-alignment masked-aligned-rep-seqs.qza
–o-tree unrooted-tree.qza
–o-rooted-tree rooted-tree.qza

qiime diversity core-metrics-phylogenetic \

–i-phylogeny mafft-fastree-out2/rooted_tree.qza
–i-table data.qza
–p-sampling-depth 100
–m-metadata-file AGP-metadata.tsv
–output-dir core-metrics-results

Plugin error from diversity:
The table does not appear to be completely represented by the phylogeny.

Hello @watson, what version of Qiime2 are you running here? Also, can you rerun the command that produced the error with the --verbose flag and post the output here? Thank you.