Features IDs in table are missing from taxonomy error after filtering

(Yakshi Ortiz) #1

Hi there,

Thank you all for your effort into creating and maintaining Qiime! I really loved Qiime1 and now I am transitioning to Qiime2.

I am using Qiime2-2019.1 using MacOS (through conda).

The general outline that I followed is next:

  1. Import demultiplexed seqs, and metadata
  2. Used vsearch to join pairs
  3. Quality filtered the sequences
  4. Dereplicate and trim seqs using denoise-16S
  5. Pick OTUs using vsearch cluster-open-reference
  6. Searched and filtered chimeras
  7. Assigned taxonomy using classify-consensus-vsearch
  8. Filtered table and seqs (to remove chloroplast, mitochondria, unassigned seqs and seqs with n=1,2,3. First I filtered the table, and using that table I filtered the sequences.
  9. Taxa collapse
  10. Barplot

Right now I am trying to run this command

qiime taxa barplot
–i-table collapsed-table-97.qza
–i-taxonomy classification-97.qza
–m-metadata-file sample-metadata.txt
–output-dir barplot-visualization

The error is the following:

Traceback (most recent call last):
  File "/Users/yakshiortiz/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in __call__
    results = action(**arguments)
  File "</Users/yakshiortiz/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-143>", line 2, in barplot
  File "/Users/yakshiortiz/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
    output_types, provenance)
  File "/Users/yakshiortiz/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 427, in _callable_executor_
    ret_val = self._callable(output_dir=temp_dir, **view_args)
  File "/Users/yakshiortiz/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_taxa/_visualizer.py", line 29, in barplot
    collapsed_tables = _extract_to_level(taxonomy, table)
  File "/Users/yakshiortiz/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_taxa/_util.py", line 42, in _extract_to_level
    collapsed_table = _collapse_table(table, taxonomy, level, max_obs_lvl)
  File "/Users/yakshiortiz/miniconda3/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_taxa/_util.py", line 20, in _collapse_table
    'taxonomy: {}'.format(missing_ids))
ValueError: Feature IDs found in the table are missing from the taxonomy: {'k__Bacteria;p__Acidobacteria;c__Solibacteres;o__JH-WHS99;f__;g__;s__',

This list keeps going a lot. I did notice that the classification file (my taxonomy) had spaces between the levels. For example:

k__Bacteria; p__Planctomycetes; c__Phycisphaerae; o__WD2101; f__; g__; s__

I already tried the solution recomended here Qiime taxa filter-table error, but it didn’t work. Do anyone have any insight into what might be happening?

In the mean time, I am working on building a phylogenetic tree (its still running; I am using raxml-rapid-bootstrap and iqtree-ultrafast-bootstrap) and I noticed that among the verbose for that step (for both methods), this next note appears around 100 times for different seqs:

NOTE/IMPORTANT WARNING: 4353904 is identical to 1016118 but kept for subsequent analysis

A few times, this other note also appeared:

NOTE/IMPORTANT WARNING: 79038 (identical to 4402382) is ignored but added at the end

Is this related to my previous error? Will this affect my results?

Thanks in advance for any suggestions,



(Yakshi Ortiz) #2


I just figured out that I don’t have to do Taxa Collapse to do the barplot. I don’t know why I had that thought really fixated in my mind. However, I still have the doubt related to the phylogenetic tree and the identical sequences.



(Nicholas Bokulich) #3

Hi @yakshi.ortiz,
Glad you sorted out the barplot error!

The phylogeny warning is just a warning from raxml — you can probably safely ignore. The reason there are identical sequences is most likely because unique ASVs become redundant after sequence masking (removing low-complexity areas of sequence after alignment) — it’s a bit of a guess but I would not be to concerned about this.

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