ERROR in qiime diversity core-metrics-phylogenetic

Hi All,
I hope you are well. I am trying to make diversity core-metrics-phylogenetic in QIIME2. Previously, import the following files generated in qiime1 to qiime2:

  • otu_table_mc2_w_tax_CFX.biom
  • rep_set_tax_assignments.txt
  • rep_set.tre unrooted -> rooted

So,
$ qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table feature-otu_table_mc2_w_tax_CFX.qza --p-sampling-depth 30 --m-metadata-file metadata --output-dir core -metrics-CFX-results /

But I have the following error:
/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/utils/validation.py:595: DataConversionWarning: Data with input dtype float64 was converted to bool by check_pairwise_arrays.
warnings.warn (msg, DataConversionWarning)
Traceback (most recent call last):
File “/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_diversity/_alpha/_method.py”, line 46, in alpha_phylogenetic
tree = phylogeny)
File “/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/diversity/_driver.py”, line 170, in alpha_diversity
counts, otu_ids, tree, validate, single_sample = False)
File “/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/diversity/alpha/_faith_pd.py”, line 136, in _setup_faith_pd
_validate_otu_ids_and_tree (counts [0], otu_ids, tree)
File “/home/patricia/miniconda2/envs/qiime2-2019.1/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 = 2): New.CleanUp.ReferenceOTU989 New.CleanUp.ReferenceOTU2438

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py”, line 274, in call
results = action (** arguments)
File “</home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-375>”, line 2, in core_metrics_phylogenetic
File “/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 458, in callable_executor
outputs = self._callable (scope.ctx, ** view_args)
File “/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_diversity/_core_metrics.py”, line 55, in core_metrics_phylogenetic
metric = ‘faith_pd’)
File “</home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-464>”, line 2, in alpha_phylogenetic
File “/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 365, in callable_executor
output_views = self._callable (** view_args)
File “/home/patricia/miniconda2/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_diversity/_alpha/_method.py”, line 50, in alpha_phylogenetic
raise skbio.tree.MissingNodeError (message)
skbio.tree._exception.MissingNodeError: All feature_ids must be present as tip names in phylogeny. feature_ids not corresponding to tip names (n = 2): New.CleanUp.ReferenceOTU989 New.CleanUp.ReferenceOTU2438

I do not understand how I could solve it.
I really appreciate your assistance!
Thank you
Patricia

Hello Patricia,

Thanks for posting that full error message. Here’s the core error:

skbio.tree._exception.MissingNodeError: All otu_ids must be present as tip names in tree .

Looks like the tree is missing some OTUs! And if we read on, we can see which OTUs are missing in the tree:

otu_ids not corresponding to tip names (n = 2): New.CleanUp.ReferenceOTU989 New.CleanUp.ReferenceOTU2438

Any idea why the tree might be missing these OTUs?

Colin

P.S. Using --p-sampling-depth 30 is really low! Having only 30 reads per sample makes it hard to compare them. I usually use 1000 as a minimum, but hope for over 10,000 reads per sample.

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