# Features IDs in table are missing from taxonomy error after filtering
**URL:** https://forum.qiime2.org/t/features-ids-in-table-are-missing-from-taxonomy-error-after-filtering/9058
**Category:** Technical Support
**Tags:** taxonomy, feature-table
**Created:** [March 29, 2019, 6:18pm UTC](https://forum.qiime2.org/t/features-ids-in-table-are-missing-from-taxonomy-error-after-filtering/9058 "2019-03-29T18:18:53Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@yakshi.ortiz](https://forum.qiime2.org/u/yakshi.ortiz)
#### Post date: [March 29, 2019, 6:18pm UTC](https://forum.qiime2.org/t/features-ids-in-table-are-missing-from-taxonomy-error-after-filtering/9058/1 "2019-03-29T18:18:53Z")
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 "", 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](https://forum.qiime2.org/t/qiime-taxa-filter-table-error/3947), 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
---
### Author:  [@yakshi.ortiz](https://forum.qiime2.org/u/yakshi.ortiz)
#### Post date: [March 29, 2019, 9:46pm UTC](https://forum.qiime2.org/t/features-ids-in-table-are-missing-from-taxonomy-error-after-filtering/9058/2 "2019-03-29T21:46:04Z")
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
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [March 29, 2019, 9:55pm UTC](https://forum.qiime2.org/t/features-ids-in-table-are-missing-from-taxonomy-error-after-filtering/9058/3 "2019-03-29T21:55:04Z")
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.