Error with qiime diversity core-metrics-phylogenetic

Hi all,

I imported a rep_set.fna file as FeatureData[Sequence] and a biom table as BIOMV210 format to QIIME2 and was able to align my sequences and go through the Moving Pictures tutorial without any issues until coming to the qiime diversity core-metrics-phylogenetic step.

The .fna and .biom were both created in QIIME1, and when I do the diversity metrics, I get the following error:

All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n=1744):


I’m attaching the original .fna and .biom files in hopes that someone can point me in the right direction!

.fna file:
biom file:

Thanks so much :slight_smile:

Hi there @leahtee - we aren’t able to reproduce that qiime diversity core-metrics-phylogenetic step, since we don’t have your metadata file.

Either way, I suspect it might be related to your numeric Feature IDs - my guess is that they are being converted to string representations of numbers in some places, and not in others (10 vs '10'). If you send us the Artifacts necessary to rerun the qiime diversity core-metrics-phylogenetic, as well as the metadata, that would be ideal. Thanks! :qiime2:

Hi @thermokarst! Thanks for getting back to me. I've attached the mapping, table and tree!

I really appreciate the help!

2016DataMapping.tsv (1.7 KB)
rooted-tree.qza (36.8 KB)

1 Like

Thanks for the additional info, @leahtee!

The FeatureTable[Frequency] that you attached doesn't quite match this statement. According to the artifact's provenance, the table was produced by running the dereplicate-sequences method in the q2-vsearch plugin, back in April:


While your FeatureData[Sequence] was created by an import action, but in June:


Any chance you might have just gotten some files mixed up in your analysis folder? The reason you are seeing the error message about feature IDs is because none of the IDs overlap - your feature table has IDs that aren't found in your phylogenetic tree. One explanation is that these artifacts are derived from entirely different analyses. Another solution would be to use the FeatureData[Sequence] that was returned alongside the table from the dereplication step.

Does that make sense? Let us know if we can provide some more detail!

Thanks! :t_rex: :qiime2:

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