Plugin error from taxa - qiime feature-table group - qiime taxa barplot

Technical Support
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1

Hello! I have some microbiota samples and the regular qiime box plot gives this by sample ID (or treatment, etc). Using the command below, I have no problems:

qiime taxa barplot
–i-table table.qza
–i-taxonomy taxonomy.qza
–m-metadata-file sample-metadata.tsv
–o-visualization taxa-bar-plots.qzv

I would like to create a stacked averaged box plot with each of my groups rather than viewing each sample individually (that is very overwhelming and doesn’t give me much meaningful information. I have tried to make a new grouped table.qza with the below command, which runs successfully:

qiime feature-table group
–i-table table.qza
–p-axis sample
–m-metadata-file sample-metadata.tsv
–m-metadata-column “TreatmentxDietxSex”
–p-mode sum
–o-grouped-table byTreatmentDietSex-table.qza

RESULTING QIIME MESSAGE: Saved FeatureTable[Frequency] to: byTreatmentDietSex-table.qza**

Then I try to make the box plot again with this new by “TreatmentDietSex-table.qza” table from above and get the following error message that I can’t seem to decipher.

qiime taxa barplot
–i-table byTreatmentDietSex-table.qza
–i-taxonomy taxonomy.qza
–m-metadata-file sample-metadata.tsv
–o-visualization taxa-bar-plots-byTreatmentDietSex.qzv

RESULTING ERROR MESSAGE
Plugin error from taxa:
Sample IDs found in the table are missing in the metadata: {‘Probiotic.CD.F’, ‘Placebo.WD.M’, ‘Placebo.CD.M’, ‘Placebo.CD.F’, ‘Probiotic.CD.M’, ‘Placebo.WD.F’, ‘Probiotic.WD.M’, ‘Probiotic.WD.F’}.
Debug info has been saved to /var/folders/l0/mc4jmsx15kbb1nkb7f_kvqjm0000gn/T/qiime2-q2cli-err-44ufubei.log

When I open the metadata, those sample IDs are present in the “TreatmentxDietxSex” column so the error message isn’t making much sense. Perhaps I am just missing an extra bit of code to make the bar chart from this grouped data by a specific column in the metadata?

I have tried --m-metadata-column “TreatmentxDietxSex” \ but it doesn’t like that command (tells me “no such option”)

Hopefully, this is something easy and me being new at this screwed something up. I really hope it is possible to get the stacked bar charts with qiime.

TIA!
Elizabeth

2

Hi!
I encountered the same issue more than a month ago. I was surprised since I followed exactly the same steps you did and it worked for me in older versions of Qiime2 but not in the latest version.
The solution was to collapse a metadata as well - I did a new smaller one with groups in the Sample-ID column instead of real ids of the samples and then removed dublicates form this new metadata file (not from my real metadata file) and used it only to create barplots. Hope that will help you.

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3

And here is an example of what @timanix is suggesting regarding the new metadata file from another post with the same question.

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4

Great, thank you for the example on how to manipulate the metadata file. It helped me visualize what I need to be doing here :slight_smile:

5

Thanks for your help @timanix!!

Apologies for the delay, but I did what you said and created a new metadata file just for that step with my groupings as sample IDs (image attached). Then I was able to manipulate the command as shown below (for future people who have this problem):

barplot VISUALIZATION BY TreatmentxDietxSex ("TDS")
qiime feature-table group
--i-table table.qza
--p-axis sample
--m-metadata-file sample-metadata.tsv
--m-metadata-column "TreatmentxDietxSex"
--p-mode sum
--o-grouped-table byTreatment-table.qza
qiime taxa barplot
--i-table byTDS-table.qza
--i-taxonomy taxonomy.qza
--m-metadata-file sample-metadatabyTDS.tsv
--o-visualization taxa-bar-plots-ByTDS.qzv

Snip20200211_167

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