I imported an taxon count table (tsv) by converting to biom and then importing to qiime. I imported a newick file of corresponding taxa (plus extra tips) via
qiime import. When I run
qiime diversity core-metrics-phylogenetic, I get the following error:
/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/31e4fc74/lib/python3.6/site-packages/sklearn/metrics/pairwise.py:1575: DataConversionWarning: Data was converted to boolean for metric jaccard warnings.warn(msg, DataConversionWarning) Traceback (most recent call last): File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/31e4fc74/lib/python3.6/site-packages/q2_diversity/_alpha/_method.py", line 54, in alpha_phylogenetic tree=phylogeny) File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/31e4fc74/lib/python3.6/site-packages/skbio/diversity/_driver.py", line 170, in alpha_diversity counts, otu_ids, tree, validate, single_sample=False) File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/31e4fc74/lib/python3.6/site-packages/skbio/diversity/alpha/_faith_pd.py", line 136, in _setup_faith_pd _validate_otu_ids_and_tree(counts, otu_ids, tree) File "/ebio/abt3_projects/software/dev/ll_pipelines/llmgp/.snakemake/conda/31e4fc74/lib/python3.6/site-packages/skbio/diversity/_util.py", line 104, in _validate_otu_ids_and_tree " ".join(missing_tip_names))) skbio.tree._exception.MissingNodeError: All ``otu_ids`` must be present as tip names in ``tree``. ``otu_ids`` not corresponding to tip names (n=1928): s__Agathobacter_sp900317585 s__Collinsella_sp900544725 s__Bacteroides_clarus s__CAG-83_sp001916855 s__Collinsella_sp900543515 s__CAG-485_sp900554845 s__UBA7160_sp002491565 ...
If I export both the feature table .qza & tree .qza files, I see that all of these labels actually overlap, so why am I getting this error?? According to qiime, ~20 of the “features” overlap between the count table and the tree. AFAIK, there’s no way to easily get the intersect of features in a count table and tree artifact, correct? That would be helpful in situations like this.
qiime2-2019.10 installed via conda.