Error when generating taxa barplot

Technical Support
1

Good morning all,

I am using de qiime2 classifier and the 138 version Silva, and after training and testing it, it resulted in a qzv that seemed that the process had gone well (I will upload the qzv), but then I tried to generate the taxa barplot and I get an error really extense.

I have read several post looking for someone with same issue, and I just found that some people get a similar error message but in a step before, when they try to do the first classification, so I am confused because my classification seems good.

Classifier

Files

  1. table.qzv (477.0 KB)
  2. taxonomy300.qzv (2.4 MB)

Script

qiime feature-classifier extract-reads
--i-sequences silva-138-99-seqs.qza
--p-f-primer GCTGACTGACT
--p-r-primer CCAATTACCATA
--p-trunc-len 300
--o-reads ref-seqs99-300.qza

qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads ref-seqs99-300.qza
--i-reference-taxonomy silva-138-99-tax.qza
--o-classifier silva-138-99-nb-classifier300.qza

qiime feature-classifier classify-sklearn
--i-classifier silva-138-99-nb-classifier300.qza
--i-reads ref-seqs99-300.qza
--o-classification taxonomy300.qza

qiime metadata tabulate
--m-input-file taxonomy300.qza
--o-visualization taxonomy300.qzv

qiime taxa barplot
--i-table table.qza
--i-taxonomy taxonomy300.qza
--m-metadata-file sample-metadata.tsv
--o-visualization taxa_bar_plots300.qzv

THE ERROR MESSAGE:

c2b5c58d0b0423', '599fb2e63b21eb43c9731718c0dfe3da', '67ad746811ee91edb91baef0bb7d2ca3', '8cfa2f4b46ced246b229f70d2c637ef3', '72a3c0b6f36f15367dd845e4da008a99', '7205c9bb40c9ee0df7c876a0c6ec15e1', '6a83897662758a7223d5bee10c6089a0', '7057b294818f2e10d978c5e44d53d070', '4d22042e2b7dbc5e5a0004ba2b015407', '9840ffdcd22dbf938761bc8fa7a25dc2', 'd6245367218b22810897ed8821b5abcf', 'e5e51f1f8b78529458b538d7aa1d8a6e', '071fbc07754ec1434890653ae9ed5819', '00d569cddd73235e1ce2211c71caa5a8', 'bba70167503afc774f0d2a573df8bd5c', 'ebf48de793de59e28721c87f73eb4388', '37b7187a9400605c0e3ee6167fed62e8', '8934407c4535894d68bfec63da6b79cb', '6a40aec86a05cc395f51f4b14877de76', 'f64da5670a366392ce0d251d38e7206f', 'e790f7e0e4a14394400d286e533c5e28', '990af1152ff34a5dbd356b275f0bb7cc', 'fbe50706cd383f0078c6f42055030f42', '031c478e4a57ac0a31946338e4d1b493', '71c715d1507784654659e6c0142c70be', 'ea438813e3e6ae4f9653e9f054285736', '0ead84d42b42c6a5b10ab1828f3294cd', '0aa4bbe111c6f65efd611f5de07d88b4', '336612853adf04ce44df2036647d17ba', '3ccdad6614d2cfa378482bcf57fbf958', 'ab7d0b54eadb4a25ed7bb1529e055cfe', 'b6ab30e2fc49045e5aba0f206ee46449', 'b9cc5cb998c194b30ac6f8a9c9a86e6e', 'a63edeb784c8cafdb2769f856aeb1d40', '9d0e245ac6a66382d9eeb39fc7ad5c57', '2bdb8c5dcdd3b7fe633d3c6b0d4d8c1c', '45c1ea08f60b111d3ce8843ab86ce6da', '31ff4337d2a5ab83fb6757a1bc475350', 'c55ff2f7aa3afa3f3b87fea42bbab82f', '2e43dfb7dea61ca57f2a7a5e3344d9ed', '85858f2ac667191d3b8a613ad09e6c05', 'e4857e869e2a1d8947ce27958833c0bb', '64bd8f634936c8e425f5d283082c0e90', '6ef26a44baa109da6b3d7cfefd4474a1', '549b215a33fb06c64727368e7fad8d5f', 'afaf466767d2bb1addc876490ae4e5fb', '5a90a5746e453f6628c796cc05326b47', '405136b2e75ffe035817b00f2b69b964', 'b847aad56ae52d2d06983ba076918003', '8a063b6ad07939cc2ec220d6c457d4ba', '195bec6fe55eb023ffc71ce49fbf7730', '2c180daf57b293a55aece42e990bafac', '82775524a1e1fa1392ee390d6084ae40', '90a8b131525cbc924cb692910f4072ab', '69dac3aac5b211625f4492edf9fed3a1', 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Debug info has been saved to /tmp/qiime2-q2cli-err-q2d313xr.log
2

Hello!

The error says that IDs from your table do not correspond to IDs from your taxonomy file. If you will check it, you notice it as well.

The issue is in this step:

qiime feature-classifier classify-sklearn
--i-classifier silva-138-99-nb-classifier300.qza
--i-reads ref-seqs99-300.qza
--o-classification taxonomy300.qza

I guess you should use rep-seq.qza file (representative sequences) instead of reference sequences for classification.

3

you are absolutely right, it fixed it. But can I ask you a question, why if in that step i used the wrong input the qzv was generated and only showed an error in the generation of the taxa barplot?

Thank you in advance.

4

Because plugin itself do not know exactly which sequences user wants to classify. Technically, since sequences were provided in the right format, classifier assigned taxonomy to it with no issues. However, for taxonomy barplot, feature ids from table and taxonomy file should be the same, and error was occurred when plugin did not find ids from feature table in taxonomy file, which was created based on reference sequences instead of representative.

2 Likes
5

Thanks a lot, this solved it !

6

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