Thanks for sending the files. I've checked them out, and as far as I can tell they seem perfect! The taxonomy's features match perfectly with the table's features, and the table's samples match perfectly with the sample metadata's samples.
However, reading through things again, I think I might have discovered the reason you were getting an error. The command you posted in your first comment above includes the following line:
I suspect that
hs_sed_table.tsv is the wrong file to use here. Since your command did not trigger an error about this file not existing, we can conclude it exists I'm guessing that this is not your sample metadata file, but is instead a TSV (tab-separated values) representation of your feature table.
If this is the case, this explains why you got the "
No samples in the feature table are present in the sample metadata" error: BIOM tables stored in TSV format usually have features as the row indices instead of samples, so Empress is interpreting
hs_sed_table.tsv as a sample metadata file where all the "sample IDs" are really feature IDs (e.g. "
Long story short, I think you should be able to fix this command and get Empress working if you change the
--m-sample-metadata-file parameter to point to
...or wherever your sample metadata file is located.
Let me know if this fixes things! If not, we can troubleshoot further.