Hello Everyone,
I hope everyone is well and healthy. I am attempting to Train my own classifier using MaarjAM database and have been at it for 10 hrs straight and I am still working on it needless to say I need help.
I have following the qiime2 tutorial for Training Feature Classifier
and I have designed my own FeatureData[Sequence] using the code below
(qiime2-2020.2) Calvin-Cornells-MacBook-Pro:Taco eyehillentertainment$ qiime tools import --type 'FeatureData[Sequence]' --input-path MercatorValidFasta.fa --output-path please_work.qza
Imported MercatorValidFasta.fa as DNASequencesDirectoryFormat to please_work.qza
and I have 'FeatureData[Taxonomy]' using the code see below
(qiime2-2020.2) Calvin-Cornells-MacBook-Pro:Taco eyehillentertainment$ qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path tax_maybe.txt --output-path please_work_taxa_please.qza
Imported tax_maybe.txt as HeaderlessTSVTaxonomyFormat to please_work_taxa_please.qza
However I skipped the next step of Extract reference reads and gone to Train the classifier which completed and I used the code see below
(qiime2-2020.2) Calvin-Cornells-MacBook-Pro:Taco eyehillentertainment$ qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads please_work.qza --i-reference-taxonomy please_work_taxa_please.qza --o-classifier please_god_work_class.qza
Saved TaxonomicClassifier to: please_god_work_class.qza
However it is when I run into Testing the classifier i run into problems I used the code below
(qiime2-2020.2) Calvin-Cornells-MacBook-Pro:Taco eyehillentertainment$ qiime feature-classifier classify-sklearn --i-classifier please_god_work_class.qza --i-reads maybe_rep-seqs.qza --o-classification taxonomy.qza
**t got the error Plugin error from feature-classifier:
this classifier does not support confidence values
I have looked through almost all of the other forums and topics in search of the answer but I haven't found any and after 10 hrs of continuously working on it I am getting really worried therefore if someone could please help me that would be amazing
Here is my --verbose code for it
Additionally I have semicolon's between each of the taxa levels (e.g between g_; s_)
Here is the txt file for my FeatureData[Taxonomy]
tax_maybe.txt (44.1 KB)
As a result if someone could please help me solve my specific problem it would be amazing and be so much appreciated,
Thank you very much and if you need more info most defiantly let me know
And the txt version of my FeatureData[Sequence]' (please note it is within the fasta format its just for this message/post it is in txt
MercatorValidFasta copy.txt (284.6 KB)
Therefore if someone could please help me in solving this specific problem it would be greatly appreciated and it would be a lot because I am getting very stressed. Thank you very much