Features IDs in table are missing from taxonomy error after filtering

feature-table
taxonomy
(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
–verbose
–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

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(Yakshi Ortiz) #2

Hi,

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.

Yakshi

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(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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