Issue with Barplot Visualization: Feature IDs Mismatch.

Hi all,
I am a new user of QIIME2, currently using the QIIME 2 amplicon distribution for taxonomic classification using the alignment-based 'classify-consensus-blast' method. I have installed QIIME2 using conda. After successfully running the classification command, I encountered an issue while attempting to visualize a bar plot. Here are the details:

Command Used:

for taxonomic classification

qiime feature-classifier classify-consensus-blast --i-query dada2_rep_set.qza --i-reference-taxonomy silva-138-99-tax.qza --i-reference-reads silva-138-99-seqs.qza --o-classification taxonomy_blast.qza --o-search-results taxonomy_search.qza

for plotting barplot

qiime taxa barplot --i dada2_table.qza --i-taxonomy silva-138-99-tax.qza --m-metadata-file metadata.tsv --o-visualization taxa-bar-plots.qzv


While the classify-consensus-blast command generated the taxonomy_blast.qza output correctly, I encountered an error when attempting to plot a barplot.

None of the feature IDs present in the feature table match those in the silva-138-99-tax.qza taxonomy file, which was downloaded from the QIIME 2 website.

The error states that "The Feature IDs found in the table are missing from the taxonomy."


Upon visualizing both the silva-138-99-tax.qza taxonomy file and my feature table, I noticed a significant difference in the structure of the feature IDs between the two files. I've attached those files for reference. I've attached the screenshots of the files for reference.

I'm reaching out for assistance as I'm unsure what steps to take next. Could you please advise on what might have gone wrong in this process?

Hello and welcome to the forum!

I think, I am a little bit confused about what you are going to achieve, but I will try my best to sort it out.

The source of my confusion is:

You already classified your sequences with the blast. Then you are downloading silva taxonomy file. But if your goal is to create a taxonomy barplot based on blast annotations you obtained, your command should be:

qiime taxa barplot \
  --i-table dada2_table.qza \
  --i-taxonomy taxonomy_blast.qza \
  --m-metadata-file metadata.tsv \
  --o-visualization taxa-bar-plots.qzv

Hope that it will help.



Thank you so much for your response!! It got solved. I got confused upon which input file to provide. I'm still new to using QIIME and currently exploring its functionalities. Sorry for the trouble.