hello everyone,
when i Train myself Naive Bayes classifiers,I input the following code"time qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads ref-seqs.qza --i-reference-taxonomy ref-taxonomy.qza --o-classifier classifier.qza"
But it comes error:
Plugin error from feature-classifier:
not enough values to unpack (expected 2, got 0)
Debug info has been saved to /tmp/qiime2-q2cli-err-hr0h_6ec.log.
The qiime2-q2cli-err-hr0h_6ec.log appear like this:
"/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_feature_classifier/classifier.py:102: UserWarning: The TaxonomicClassifier artifact that results from this method was trained using scikit-learn version 0.24.1.
It cannot be used with other versions of scikit-learn. (While the classifier may complete successfully, the results will be unreliable.)
warnings.warn(warning, UserWarning)
Traceback (most recent call last):
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in fit_classifier_naive_bayes
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_feature_classifier/classifier.py", line 330, in generic_fitter
pipeline = fit_pipeline(reference_reads, reference_taxonomy,
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/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 also checked the forum, I can't find my ref-seqs.qza and ref-taxonomy.qza file
Hi @sj_Liu ,
This error is quite common when attempting to train a classifier with a custom database, usually either due to uneven ranks in your taxonomy or because the sequence and taxonomy headers do not match. Please see these pre-existing topics for troubleshooting advice:
https://forum.qiime2.org/search?q=Plugin%20error%20from%20feature-classifier%3A%20not%20enough%20values%20to%20unpack
Good luck!
Thank you!But i have read the forum answer before and checked my ref-seqs.qza and ref-taxonomy.qza file.I think there are no above problem.
This is my taxonomy file:"Feature ID Taxon
Vr-33 k_Bacteria; p_Firmicutes; c_Negativicutes; o_Selenomonadales; f_Veillonellaceae; g_Veillonella; s_Veillonella ratti
Va-47 k_Bacteria; p_Firmicutes; c_Negativicutes; o_Selenomonadales; f_Veillonellaceae; g_Veillonella; s_Veillonella atypica
Vp-99 k_Bacteria; p_Firmicutes; c_Negativicutes; o_Selenomonadales; f_Veillonellaceae; g_Veillonella; s_Veillonella parvula
Pd-43 k_Bacteria; p_Firmicutes; c_Clostridia; o_Clostridiales; f_Peptostreptococcaceae; g_Peptoclostridium; s_Peptoclostridium difficile
Lr-97 k_Bacteria; p_Firmicutes; c_Bacilli; o_Lactobacillales; f_Lactobacillaceae; g_Lactobacillus; s_Lactobacillus rhamnosus
Ec-5 k_Bacteria; p_Proteobacteria; c_Gammaproteobacteria; o_Enterobacteriales; f_Enterobacteriaceae; g_Escherichia; s_Escherichia coli
Ef-64 k_Bacteria; p_Firmicutes; c_Bacilli; o_Lactobacillales; f_Enterococcaceae; g_Enterococcus; s_Enterococcus faecium
Eca-2 k_Bacteria; p_Firmicutes; c_Bacilli; o_Lactobacillales; f_Enterococcaceae; g_Enterococcus; s_Enterococcus casseliflavus
Cb-62 k_Bacteria; p_Firmicutes; c_Clostridia; o_Clostridiales; f_Clostridiaceae; g_Clostridium; s_Clostridium butyricum
Ca-1 k_Bacteria; p_Proteobacteria; c_Gammaproteobacteria; o_Enterobacteriales; f_Enterobacteriaceae; g_Citrobacter; s_Citrobacter amalonaticus
Bd-24 k_Bacteria; p_Actinobacteria; c_Actinobacteridae; o_Bifidobacteriales; f_Bifidobacteriaceae; g_Bifidobacterium; s_Bifidobacterium dentium
Br-81 k_Bacteria; p_Actinobacteria; c_Actinobacteridae; o_Bifidobacteriales; f_Bifidobacteriaceae; g_Bifidobacterium; s_Bifidobacterium breve
Ba-80 k_Bacteria; p_Actinobacteria; c_Actinobacteridae; o_Bifidobacteriales; f_Bifidobacteriaceae; g_Bifidobacterium; s_Bifidobacterium adolescentis
Ac-115 k_Bacteria; p_Firmicutes; c_Clostridia; o_Clostridiales;f_Lachnospiraceae; g_Anaerostipes; s_Anaerostipes caccae
"
This is my ref-seqs file:">Vr-33
TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTTTCATAAGTCTGTCTTAAAAGTGCGGGGCTTAACCCCGTGAGGGGATGGAAACTATGGAACTGGAGTATCGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACGACAACTGACGCTGAGGCGCGAAAGCCAGGGGAGCGAACG
Va-47
TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATTGGTCAGTCTGTCTTAAAAGTTCGGGGCTTAACCCCGTGATGGGATGGAAACTGCCAATCTAGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACTGACGCTGAGGCGCGAAAGCCAGGGGAGCGAACG
Vp-99
TACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGATAGGTCAGTCTGTCTTAAAAGTTCGGGGCTTAACCCCGTGATGGGATGGAAACTGCCAATCTAGAGTATCGGAGAGGAAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGACTTTCTGGACGAAAACTGACGCTGAGGCGCGAAAGCCAGGGGAGCGAACG
Pd-43
TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCNGTAGTAAGCTCTTGAAACTGGGAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAAC
Lr-97
TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCTCGGCTTAACCGAGGAAGTGCATCGGAAACTGGNAAAACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAA
Ec-5
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAA
Ef-64
TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAA
Eca-2
TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAA
Cb-62
TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGTGGATATTTAAGTGGGATGTGAAATACCCGGGCTTTAACCTGGGTGCTGCATTCCAAACTGGATATCTAGAGTGCAGGAGAGGAAAGGAGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAATACCAGTGGCGAAGGCGCCTTTCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGGAGCAAA
Ca-1
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAAC
Bd-24
TACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGCCCATCGCTTAACGGTGGGTCTGCGCCGGGTACGGGCGGGCTGGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAAC
Br-81
TACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAAC
Ba-80
TACGTAGGGTGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTCGTCGCGTCCGGTGTGAAAGTCCATCGCTTAAACGGTGGATCCGCGCCGGGTACGGGCGGGCTTGAGTGCGGTAGGGGAGACTGGAATTCCCGGTGTAACGGTGGAATGTGTAGATATCGGGAAGAACACCAATGGCGAAGGCAGGTCTCTGGGCCGTCACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAA
Ac-115
TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGTGCGTAGGTGGCATGGTAAGTCAGAAGTGAAAGCCCGGGGCTTAACCCCGGGACTGCTTTTGAAACTGTCATGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTCACTGACACTGATGCACGAAAGCGTGGGGAGCAAAC
"
So i think my sequence and taxonomy headers match.I can't understand what is uneven ranks in my taxonomy?
Thank you for your kindness reply.Hope your can help me again! Thanks！
you could check for invisible characters
the number of ;-separated levels in each taxonomic lineage
I also suggest running the command qiime tools validate on both files to see what information you get.
Thank you！I checked my files again followed your advice.Then i found why the error appeared.Thank you very much!
for others who are reading this topic later, could you please explain what the issue was?
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