RE: readytowear SILVA 138 Training Error

Hi Nicholas. Could you please explain ahow to filtering a taxonomy, so you can remove IDs not in the sequences and re-create human-stool weights?

Hi @imonteroo,

If you run qiime rescript filter-taxa --help, you'll see that you can simply provide the sequence file to the --m-ids-to-keep-file parameter. Then you provide your taxonomy file with the --i-taxonomy parameter. This will remove any taxonomy with IDs that are not found within the sequence file.

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Thank you Mike. I tired the next code

qiime rescript filter-taxa --m-ids-to-keep-file silva-138.1-ssu-nr99-seqs-V3V4-uniq.qza --i-taxonomy readytowear-master/data/silva_138_1/full_length/human-stool.qza --o-filtered-taxonomy human-stool-V3V4.qza

but "human-stool.qza" is not a FeatureData[Taxonomy] file, is an FeatureTable[RelativeFrequency].

I am trying to create a silva-138.1-ssu-nr99-V3V4-stool-classifier.qza

I could create silva-138.1-ssu-nr99-V3V4-classifier.qza but I don't have human-stool-V3V4.qza so error "Number of priors must match number of classes" appears.

I could create silva-138.1-ssu-nr99-stool-classifier.qza because I have humann-stool.qza with full 16S from redytowear. I couldn't find the V3V4 version.

I am analyzing 16S V3V4 Illumina sequences so I think I need the V3V4 trained classifier.

Hi @imonteroo ,
If you are trying to create new weights with a different taxonomy you will need to follow this tutorial from the beginning:

The readytowear weights are built using specific taxonomies (as described in the readytowear repository) so will only work with those taxonomies.

Good luck!

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