Working with plants? Try "PLANiTS": a plant ITS reference database for QIIME2

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1

Hello QIIME2 users!

I am Elisa Banchi, a Research Fellow at the National Institute of Oceanography of Trieste, Italy.

With the University of Trieste, we have developed PLANiTS, a reference dataset for plant ITS formatted for QIIME2.

The database is available at the following link:
https://academic.oup.com/database/article/doi/10.1093/database/baz155/5722079
PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding
E Banchi, CG Ametrano, S Greco, D Stanković, L Muggia, A Pallavicini (2020)

and we have successfully applied it here:

Environmental DNA assessment of airborne plant and fungal seasonal diversity
https://www.sciencedirect.com/science/article/pii/S0048969720337700
E Banchi, CG Ametrano et al (2020)

We believe that PLANiTS represents a new, valuable resource for researchers dealing with plant DNA metabarcoding.

We will be happy to receive feedback, questions, and suggestions about the database.

Thank you!

Elisa

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2

Hello, I’m trying to use it, but I’m having problems on the training it with my seqs would you describe your steps?

3

Hello there, I’m trying to execute the command:
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads rep-seqs-dada2.qza --i-reference-taxonomy ITS2-taxonomy.qza --o-classifier classifier.qza

The --i-reference-reads is a file that I generate from a forward and a reverse fastq file after the command:
qiime deblur denoise-16S --i-demultiplexed-seqs demux.qza --p-trim-length -1 --p-sample-stats --o-representative-sequences rep-seqs.qza --o-table table.qza --o-stats deblur-stats.qza

The --i-reference-taxonomy ITS2-taxonomy.qza was imported from the PLAnITS dataset with the command:
qiime tools import --type ‘FeatureData[Taxonomy]’ --input-path /home/fabiobones/PLANiTS_29-03-2020/ITS2_taxonomy --input-format HeaderlessTSVTaxonomyFormat --output-path ITS2-taxonomy.qza

So on the fit-classifier-naive-bayes, i get this error:

Plugin error from feature-classifier:
not enough values to unpack (expected 2, got 0)

and this log file:
Traceback (most recent call last):
File “/home/fabiobones/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</home/fabiobones/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-345>”, line 2, in fit_classifier_naive_bayes
File “/home/fabiobones/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/fabiobones/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 390, in callable_executor
output_views = self._callable(**view_args)
File “/home/fabiobones/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_feature_classifier/classifier.py”, line 331, in generic_fitter
pipeline)
File “/home/fabiobones/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_feature_classifier/_skl.py”, line 31, in fit_pipeline
y, X = list(zip(*data))
ValueError: not enough values to unpack (expected 2, got 0)

I’ve looked upon a lot of similar errors on the forum, but still couldn’t figure out the solution. Can someone help me?

4

Dear Fabio,

thanks for the interest in our database!

I believe that the problem is that the classifier step should be performed to integrate taxonomy and sequences of the database itself.

https://docs.qiime2.org/2020.6/tutorials/feature-classifier/

Doing that, you produce the ITS2 classifier:

qiime tools import --type ‘FeatureData[Taxonomy]’ --input-path ITS2_taxonomy --input-format HeaderlessTSVTaxonomyFormat --output-path ITS2_taxonomy.qza

qiime tools import --type FeatureData[Sequence] --input-path ITS2.fasta --output-path ITS2.qza

qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ITS2.qza --i-reference-taxonomy ITS2_taxonomy.qza --o-classifier ITS2_classifier.qza

This classifier can now be used for taxonomic assignment of your samples.

We will be able soon to provide the classifiers for plant ITS1 and ITS2 in our github page and also here in the forum. I will keep users updated about that.

Let me know if you managed to resolve your issue.

Best,

Elisa

5

Hello, yes, I’m actually embarrassed, all this problem because I misunderstood the tutorial. Now I’m dealing with this “Segmentation fault (core dumped)” message. By what I could find out, is possible a computer performance issue, since I’m running Ubuntu on windows in a 8gb ram core i5 computer, and watching the memory usage, it reaches 100% several times.

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6

Currently trying to use the PLANiTS ITS2 classifier, however this has been made with an older version of scikits... is there a possibility to update the GitHub repository with a newly trained classifier? Currently don't have enough computational power to train the classifier locally.

Best wishes

2 Likes
7

@ElisaBanchi, if you get a chance could you review this request from a PLANiTS user?

1 Like