Beta diversity volatility plots

[saatkinson (Samantha)]

Hello,

I’m trying to run the qiime longitudinal volatility plugin on the beta diversity artifact I created using qiime diversity core-metrics-phylogenetic. I’m pretty sure this is allowed because the longitudinal tutoral says:

Multiple metadata files (including alpha and beta diversity artifacts) and FeatureTable[RelativeFrequency] tables can be used as input,

I’m using QIIME2 version 2018.11

This is the command I’ve tried:
qiime longitudinal volatility
–m-metadata-file mapping_cessation.txt
–m-metadata-file core-metrics-results/weighted_unifrac_distance_matrix.qza
–p-default-metric Distance --p-default-group-column group
–p-state-column Round
–p-individual-id-column Mouse_num
–o-visualization longitudinal_test/vis_weighted_volatility.qzv

This is the error I got:
There was an issue with viewing the artifact core-metrics-results/weighted_unifrac_distance_matrix.qza as QIIME 2 Metadata:

Artifact <artifact: DistanceMatrix % Properties([‘phylogenetic’]) uuid: 91edce49-78aa-4c79-8321-187bd0194f54> cannot be viewed as QIIME 2 Metadata.

I got the same error with unweighted.

I then tried using the output of qiime diversity beta-group significance and get a different error about metadata files needing to be encoded in UTF-8 or ASCII, I’m assuming it didn’t like the qzv format.

If you could tell me the correct way to format the command so that it runs properly that would be great.

Thanks,
Samantha

[Nicholas_Bokulich]

the longitudinal tutoral says:

Multiple metadata files (including alpha and beta diversity artifacts)

By “beta diversity artifacts” that tutorial means only those that can be interpreted as metadata, i.e., PCoA results.

You will need to either compute PCs on your distance matrix or use first-distances to convert to first distances (see tutorial for more details). Those artifacts can be used as input to volatility, but a distance matrix cannot.

I then tried using the output of qiime diversity beta-group significance and get a different error about metadata files needing to be encoded in UTF-8 or ASCII, I’m assuming it didn’t like the qzv format.

Yep, QZVs cannot be used as input to any QIIME 2 commands (though raw data can often be downloaded from QZVs and used as metadata inputs).

I hope that helps!