installing and using q2-greengenes plugin

[wasade (Daniel McDonald)]

Hi @minjoy,

Thank you for the kind words, and I'm sorry for the challenges!

Could you provide the output from pip install q2-greengenes2, and can you describe what QIIME 2 environment this was installed into?

To your questions:

@minjoy

• Is downloading the two files ('2022.10.backbone.full-length.fna.qza' and '2022.10.backbone.tax.qza') and proceeding with the rest of the process the same as creating the two files through 'If there is data other than V4'?

That should work

@minjoy

• When I download two files from online ('2022.10.backbone.full-length.fna.qza' and '2022.10.backbone.tax.qza' ), are there md5Sum values available?

Great question It wouldn't hurt to include them but we don't currently automatically compute them. I've added an issue.

@ebolyen, do you know off-hand whether md5 is necessary for .qza to assert a download is reasonable?

@minjoy, the relevant MD5s are:

$ md5sum 2022.10.backbone.full-length.fna.qza
eb2c35a194ca340fba4ce486c08747d3  2022.10.backbone.full-length.fna.qza
$ md5sum 2022.10.backbone.tax.qza
010ade1db3c86814cdd0fe61be04dc8a  2022.10.backbone.tax.qza

@minjoy

• For performing 'feature-classifier' using naïve-bayes, it only took 1-2 hours. Can it be this fast? (Of course, the speed depends on the CPU and GPU I use.)

I don't recall off hand what to expect for the performance of application of feature-classifier. Is that performance okay for your use?

@minjoy

• I'm training a classifier on V3-V4 regions using Greengenes2 using the following commands below.

These seem reasonable. For reference, the commands used to construct the release classifiers can be found here.

@minjoy

Can I have any sample data that I can test the classifier?

There are a lot of public data readily accessible in Qiita, and which can be obtained via the command line using redbiom. A tutorial on that can be found here.

All the best,
Daniel