Subtype TaxonomicClassifier is required


(Mary DuPre) #1

Hello all,

I received an error that I have been unable to solve. I understand that I am not using the correct --type format, but have been unable to find the correct format to use. If anyone can lead me to the correct format (with the full command, please) or a tutorial, that would be very helpful! Below is the section of code that brought on the error.

qiime tools import
–type FeatureData[Taxonomy]
–input-path UNITE-plus-all-contams.txt
–input-format HeaderlessTSVTaxonomyFormat
–output-path UNITE-plus-all-contams-CLASSIFIER.qza

qiime feature-classifier classify-sklearn
–i-classifier UNITE-plus-all-contams-CLASSIFIER.qza
–i-reads hits-9-9.qza
–p-confidence 0.9
–o-classification taxonomy-hits9-9-c90.qza

Plugin error from feature-classifier:

Parameter ‘classifier’ received an argument of type FeatureData[Taxonomy]. An argument of subtype TaxonomicClassifier is required.

Debug info has been saved to /var/folders/_h/xck42wn55x957rpgq54pn_ph0000gn/T/qiime2-q2cli-err-kqzks6cr.log

Thank you,

Mary Ellyn


(Nicholas Bokulich) #2

To use a machine learning taxonomy classifier, you must first train that classifier on your sequences of interest. See this tutorial. Training a classifier requires both the sequences and their taxonomy annotations. What you have done is import the taxonomy file alone — that is not a TaxonomicClassifier artifact type.

Note, you can use the other taxonomy classification methods in q2-feature-classifier with the sequence and taxonomy files (see the classify-consensus-* methods). These are based on alignment and do not need prior training.

Good luck!


(Mary DuPre) #3

Thank you for the quick response! I’m glad there was a clear answer, because I was able to continue the workflow this afternoon.

Best,
Mary Ellyn