Taxaplots error

User Support
1

Hello I am using Qiime2-2022.11
I am getting a error in the taxaplot step:
This are the commands :
qiime taxa barplot
--i-table table_.qza
--i-taxonomy taxonomy_.qza
--m-metadata-file Metadatos_.tsv
--o-visualization taxa-bar-plots_.qzv

Plugin error from taxa:

Feature IDs found in the table are missing from the taxonomy: {'e471b4d90051213a2f380260fc40378f', '6ae397141328fcc917b9a87aa5d548a3', '4c5b12e3825577cde8437df04f5536cc', 'c6d453157c99855d562c971b88788b3c', '6f61d8be1f0a019dc7e7a7ae07c54d08', '5169c226a333dcb12102eff6cd3ad818', '7fee385ad9598137793ac77c7e7c11b4', '043761376a7b4bbf5ed08e472972dd4f', '8ea54389c04fc34bcf3487220ad73af0', '950a9b08dd59529ce33fc4c92c45165b', 'c9a6fea22a7d3e590311fa5674ad44db', '1c7f2d2baa0b3c0e45c3423b4d62d091', 'b3b31167d7d79314b45e782a7939b17e', 'a70c70e204e3b5a7632b047988b6b1ef', 'a1d62669ba5f67dd079c2f7ff250f1fe', 'f66631894ca0b6bbfb15c71c0c6fde10', ' etc. etc.

I am not sure what to do.
Thanks

2

Hello @EugeniaSH,

Please see this post, from a user with an identical problem.

Thanks.

3

Thank you
I will try it.
He uses Qiime2-2023 , and I am using 2-2022.11, would that be an issue?
I noticed several different steps in the pipeline, starting on step 7 : qiime feature-table filter-samples
Thanks

4

Hello @EugeniaSH,

The version of qiime will almost certainly not be an issue. The post I linked wasn't meant to be a pipeline to follow, but rather contain an explanation of why/how your feature table and taxonomy became out of sync, which is the root of the issue here.

5

Thanks
However I am not sure how to fix it.
Any and all help will be greatly appreciated
Eugenia

6

Hello @EugeniaSH,

What filtering have you applied to the sequences that made your taxonomy? You need to apply the same filtering to your feature table.

7

Thank you,
I am sorry for the novice questions, but I am not even sure that I filter.

This is my pipeline after import :

3- qiime dada2 denoise-paired
--i-demultiplexed-seqs imported_seq.qza
--p-trunc-len-f 210
--p-trunc-len-r 210
--p-trim-left-f 0
--p-trim-left-r 0
--p-n-threads 0
--o-representative-sequences rep-seqs.qza
--o-table table.qza
--o-denoising-stats stats.qza

  1. visualize

  2. qiime feature-table summarize
    --i-table table.qza
    --o-visualization table.qzv
    --m-sample-metadata-file Metadata.tsv

  3. qiime feature-table tabulate-seqs
    --i-data rep-seqs.qza
    --o-visualization rep-seqs.qzv

  4. qiime phylogeny align-to-tree-mafft-fasttree
    --i-sequences rep-seqs.qza
    --o-alignment aligned-rep-seq.qza
    --o-masked-alignment masked-aligned-rep-seqs.qza
    --o-tree unrooted-tree-qza
    --o-rooted-tree rooted-tree.qza

  5. diversity core metrics

  6. alphararefraction
    10 alpha diversity

  7. taxonomy
    qiime feature-classifier classify-sklearn
    --i-classifier Classifier/classifier.qza
    --i-reads Classifier/ref-seqs.qza
    --o-classification taxonomy.qza

qiime metadata tabulate
--m-input-file taxonomy.qza
--o-visualization taxonomy.qzv

12 taxabar plots
qiime taxa barplot
--i-table table.qza
--i-taxonomy taxonomy.qza
--m-metadata-file Metadatos.tsv
--o-visualization taxa-bar-plots.qzv

THANK YOU

8

Hello @EugeniaSH,

You're classifying the reference-sequences in step 10. Although this will result in a very accurate classification :grinning:, this isn't what you want. You want to classify your sequences, namely rep-seqs.qza, which came out of dada2.

Let us know if this makes sense.

9

Absolutely. Makes TOTAL SENSE!

Sorry for the trouble.
Eugenia

1 Like
10

@EugeniaSH,

No need to apologize, this is what the forum is for. Let us know if the taxa bar plot works smoothly now.

11

perfectly.
Thanks again

12

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