Multiple entries after collapsing using taxa barplot

[rhmills]

Qiime2 version: 2019.1
Installation: conda

Hi,

After running the qiime taxa barplot command, and visualizing the results through the output .qzv file, there appears to be a potential error when collapsing abundances by different levels of taxonomy. The error seems to be related to when there is missing or unclear taxonomy at a higher level and trying to collapse to a lower level of taxonomy.

For example, I am looking to visualize and understand genera level differences within my samples but have two bars associated with unknown genus from the family Lachnospiraceae. One entry is:
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__

While the other entry is:
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;__

The difference here seems to be the presence or absence of a "g" when you have an unknown entry.

As the greengenes database I am using for the taxonomic assignments does not have any taxonomic entries without an identifier, I'm wondering if this is a result of parsing within the command.

The code used for the analysis is here:

!qiime feature-classifier classify-sklearn
--i-classifier ../gg-13-8-99-515-806-nb-classifier.qza
--i-reads sequences.qza
--o-classification taxonomy.qza

!qiime metadata tabulate
--m-input-file taxonomy.qza
--o-visualization taxonomy.qzv

!qiime taxa barplot
--i-table biom.qza
--i-taxonomy taxonomy.qza
--m-metadata-file ./10933_prep_3336_qiime_20170619-140801.txt
--o-visualization taxa-bar-plots.qzv

Please let me know if you have any possible explanations for this.

Thanks,
Robert

[thermokarst]

Hey there @rhmills - can you please clarify what exactly you think is an error here?

There difference between the two entries is expected --- the first one (g__) means the feature was classified to at least that level, however the DB has no annotation at that depth. The second entry means that the classification stopped at family level, there was no match at the genus level given your confidence threshold when running classify-sklearn.

[rhmills]

Thanks for the clarification! That's all I needed to know.

Thank you,
Robert