Troubleshooting: None of the feature identifiers match between the metadata and the coordinates.

Hi there!

I am trying to generate an emperor biplot and keep getting the following error message: "None of the feature identifiers match between the metadata and the coordinates. Verify that you are using metadata and coordinates corresponding to the same dataset."

Despite having read through all of the posts related to this issue, I can't seem to come to a solution and would greatly appreciate your insight and help! I have double checked the sampleIDs for all files involved and don't see an issue with those.

The version of qiime2 that I am running is qiime2-2021.11 and it was installed via Anaconda.

The exact commands that I ran are:

qiime diversity pcoa-biplot \
--i-pcoa rarefied_diversity_metrics/rarefied_1000_exp1_2/bray_curtis_pcoa_results.qza \
--i-features Output/GDM_relfreq_exp1_2_1000.qza \
--o-biplot rarefied_diversity_metrics/rarefied_1000_exp1_2/BCD_biplot_exp1_2 

qiime emperor biplot \
--i-biplot rarefied_diversity_metrics/rarefied_1000_exp1_2/BCD_biplot_exp1_2.qza \
--m-sample-metadata-file samples-to-keep_GDM_metadata_exp1_2.txt \
--m-feature-metadata-file Output/GDM_relfreq_exp1_2_1000.qza \
--o-visualization Visualization/BCD_biplot_1000_exp1_2

While I had no issue generating the pcoa-biplot, when I run the command for the emperor biplot, the full error message that I get is:

Traceback (most recent call last):
  File "/opt/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
    results = action(**arguments)
  File "<decorator-gen-459>", line 2, in biplot
  File "/opt/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/opt/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 453, in _callable_executor_
    ret_val = self._callable(output_dir=temp_dir, **view_args)
  File "/opt/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_emperor/_plot.py", line 127, in biplot
    generic_plot(output_dir, master=biplot, other_pcoa=None,
  File "/opt/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_emperor/_plot.py", line 41, in generic_plot
    viz = Emperor(master, mf, feature_mapping_file=feature_metadata,
  File "/opt/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/emperor/core.py", line 226, in __init__
    self._validate_metadata(feature_mapping_file,
  File "/opt/anaconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/emperor/core.py", line 304, in _validate_metadata
    raise ValueError('None of the %s identifiers match between the'
ValueError: None of the feature identifiers match between the metadata and the coordinates. Verify that you are using metadata and coordinates corresponding to the same dataset.

Attached are the files being used, along with the manifest file used to upload the data.
Thanks again for your time and help!

BCD_biplot_exp1_2.qza (1.5 MB)
GDM_relfreq_exp1_2_1000.txt (804.8 KB)
GDM_relfreq_exp1_2_1000.qza (330.1 KB)
samples-to-keep_GDM_metadata_exp1_2.txt (10.3 KB)
GDM_manifest2.txt (51.9 KB)

Hello @VickiM ,
Welcome to the :qiime2: forum!
So your issue is that your feature metadata file is a feature table. Feature tables have sample-ids as rows and feature-ids as columns. Feature Metadata needs to have feature ids as rows.

Usually for feature metadata a taxonomy file is used. That way the visualization knows the classification labels of the features. I am not sure what additional information you would get by using your feature table.
Hope that helps!
:turtle:

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