Problem with taxonomy

[mosmasha (Maria)]

Hello everyone!
I am new to qiime2. I have qiime2-2019.10 version, linux conda ubuntu
I complete all tasks in " “Moving Pictures” tutorial" and after
qiime taxa barplot
–i-table table.qza
–i-taxonomy taxonomy.qza
–m-metadata-file sample-metadata.tsv
–o-visualization taxa-bar-plots.qzv

I got the result that mine taxonomy, in all my 40 samples are
k__Bacteria;p__Firmicutes;c__Clostridia 100%

Bar plot didn’t split.
I will be very grateful for the help!!

[Nicholas_Bokulich]

Welcome to the forum, @mosmasha!

This sounds like it may be an issue with the taxonomy classification step, unless if you were expecting 100% Clostridia.

1. how did you classify your sequences taxonomically? (method, source of the reference/classifier, etc)
2. how many sequences do you have per sample? Were there any upstream processing issues that might cause a problem?
3. What were you expecting to see?
4. Could you share your taxa-bar-plots.qzv so that we can take a look?

There are several topics regarding taxonomy errors listed inside the following topic, these might give you some ideas of what may have gone wrong:

Frequent Questions and "Best of the QIIME 2 Forum"

The following is a list of frequently asked questions on the forum, with answers, to serve as a point of reference for forum users to quickly find answers, or for forum users and moderators to use as a reference when helping others. Note: some of these listings are collapsed lists. If you see an arrow next to a title, click the title to expand the list of topic titles related to that subject. FAQs What is a "Feature" exactly? MemoryError with q2-feature-classifier How a…

Thanks!

[mosmasha (Maria)]

Hello, Nicholas!
Thank you for your answer!
I understood my problem. I think, it was in the step:
qiime feature-classifier extract-reads,
Maybe I took the wrong section of 16s RNA (It was not V4)
When I used the full 16s RNA, the next step
(qiime feature-classifier classify-consensus-blast)
was succesful and next (qiime taxa barplot) too.

Thanks again for your reply!
To be honest, I thought I won’t get it and abandon this thing.
Now I want to continue!!!

[Nicholas_Bokulich]

Hi @mosmasha,
So glad to hear you could resolve the problem, and that it has inspired you to continue!

@mosmasha

Maybe I took the wrong section of 16s RNA (It was not V4)

Makes perfect sense — that could certainly cause the error you saw.

@mosmasha

When I used the full 16s RNA, the next step
(qiime feature-classifier classify-consensus-blast)
was succesful and next (qiime taxa barplot) too.

Perfect.

Please get in touch if you have any more concerns!