ERROR: Test the classifier, metadata tabulate

[Grace1 (Grace)]

Hi there,

I'm currently in the stage of the QIIME pipeline where I am 'testing my 16S classifier'. I'm using 515F 806R primers and Silva 132 (99). I have used this pipeline before without any problems so unsure where the error is coming from.

I've just run this code to transform the resultant taxonomy file from .qza to .qzv (I use a HPC):
qiime metadata tabulate
--m-input-file /export/home/f-k/galmoaji/CH2/CH2_taxonomy.qza
--o-visualization /export/home/f-k/galmoaji/CH2/CH2_taxonomy.qzv

But I got this error:
There was an issue with viewing the artifact /export/home/f-k/galmoaji/CH2/CH2_taxonomy.qza as QIIME 2 Metadata:
CategoricalMetadataColumn does not support values with leading or trailing whitespace characters. Column 'Taxon' has the following value: 'D_0__Bacteria;D_1__Planctomycetes;D_2__Phycisphaerae;D_3__Phycisphaerales;D_4__Phycisphaeraceae;D_5__uncultured;D_6__uncultured bacterium '

I'm not sure what the error means, and as I said before I've used this pipeline and method before with no problems so no sure what to do.

Any help would be greatly appreciated!

Thanks
Grace

[timanix (Timur Yergaliyev)]

Hi!
Here the commands to fix it

Taxonomy analysis error

Hi! I found on this forum and a little changed this way to fix it: !qiime feature-classifier classify-sklearn \ --i-classifier training-feature-classifiers/classifier.qza \ --i-reads rep-seqs.qza \ --o-classification taxonomy.qza !qiime tools export \ --input-path taxonomy.qza \ --output-path taxonomy-with-spaces !qiime metadata tabulate \ --m-input-file taxonomy-with-spaces/taxonomy.tsv \ --o-visualization taxonomy-as-metadata.qzv !qiime tools export \ --input-path taxonomy-a…

[Grace1 (Grace)]

Thanks for that! I will give that a go.

Just having a look at the code:
The first metadata tabulate code
!qiime metadata tabulate
--m-input-file taxonomy-with-spaces/taxonomy.tsv
--o-visualization taxonomy-as-metadata.qzv

Where does the taxonomy.tsv file come from? is that my own metadata file or the taxonomy file from Silva?

I was also wondering if the ! are needed?

Thanks

Grace

[Grace1 (Grace)]

Hi @timanix,

The code worked!

Thanks very much!

Got some great taxa barplots now

Grace

[timanix (Timur Yergaliyev)]

I guess, you already figured out everything by your own, sorry for the late answer.
'!' - they are not necessary if you are working from the terminal. I copied it from Jupyter Notebook.
Good luck with further analysis