Importing Phylogenetic Tree from MEGAN

Technical Support
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Hi! Just to follow up, I am not convinced the underscores being cast to spaces is the issue. I am confused as to what the problem is, actually. Here is my workflow:

Download .biom file from MEGAN -> convert .biom file to FeatureTable[Frequency]

qiime tools import \
  --input-path Comparison-Taxonomy.biom \
  --type 'FeatureTable[Frequency]' \
  --input-format BIOMV100Format \
  --output-path Comparison-Taxonomy.qza

This feature table lists the features as their NCBI taxonomic IDs and not as their written-out names (e.g. 291644 instead of d__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__Bacteroides salyersiae). I know this because when I use feature-table summarize to convert the FeatureTable[Frequency] to a .qzv file, the features are listed as these numbers rather than the taxa names.

(I don't know if this is useful information, but to make bar plots, I created a file I named taxonomy.txt with each taxon ID associated with its written-out name and imported it as FeatureData[Taxonomy]. I then supply it in the --i-taxonomy option for qiime taxa bar plot so the bar plot has names instead of numeric IDs.)

Here is the strange part. I wrote a short script to take every numeric ID present in my .biom file and see if it is present in the ncbi.tre file. The ncbi.tre file, attached earlier above, only lists phylogeny with these numeric IDs rather than spelled-out names. Every single ID present in the .biom file is also present in the ncbi.tre file. So this is where I am stumped as to why there is an issue.

Here is how I am importing the ncbi.tre file, which is in Newick format and is a rooted tree.:

qiime tools import \
  --input-path ncbi.tre \
  --output-path rooted-tree.qza \
  --type 'Phylogeny[Rooted]'

qiime diversity core-metrics-phylogenetic \
  --i-phylogeny rooted-tree.qza \
  --i-table Comparison-Taxonomy.qza \
  --p-sampling-depth 6655889 \
  --m-metadata-file Comparison-metadata.txt \
  --output-dir core-metrics-results

Any insight or ideas would be so so appreciated.

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