Hi @Mehrdad,
The answer to your questions have already been answered very early on in this thread.
@colinbrislawn mentioned:
Your original command was right, except instead of the classifier.qza which is something you use to create a taxonomy file, you want to put as input the actual taxonomies file which is specific to your dataset. The classifier.qza itself can be used on any other dataset and it holds no information regarding your data.
You had --i-table TableDenoisedLibA.qza which is correct, and now
you need to give --i-taxonomy taxonomylibA.qza. The rest of your commands were right.
For your own learning sake, instead of trying every combination of files you have until something sticks I would -once again- urge you to go over the Overview tutorial and a few of the example tutorials thoroughly until you properly understand the workflows you are performing, otherwise you will learn nothing and will have the same questions next time you run another analysis. And as you might imagine, repetitive and redundant questions on the forum are not ideal and are less likely to get a proper response.
For example, as @llenzi was hinting at, a good starting point would be to check to see what your artifacts are and what it is that the script is expecting from you.
Check out what you see when you run qiime tools peek classifier.qza and qiime tools peek TableDenoisedLibA.qza, or check out the provenance tab of those files in qiime2view. Now compare those formats to the expected file formats from the help file. That is one fast way to figure out which type of file you need to be passing. You can also look at the tutorial examples to see exactly which files are being passed through.
Anyways, good luck with the rest of the workflow!
key, but the sign was switched off! It is not my fault.
