Hello @cherman2,
Thank you for your help and support.
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It looks like you already made sure that you are not filtering out sequences but I would first make sure that you are not discarding too many samples with your sampling depth. Mike Robson does a great job explaining why here: The table does not appear to be completely represented by the phylogeny.
Indeed, I made sure to retain a maximum of samples, I chose a sampling depth of 24985 and Retained 124,925 (72.37%) features in 5 (100.00%) samples at the specifed sampling depth. So I think I don't loose too many information, right ?
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My next suggestion would be to make sure the names are the same in your rooted tree ID’s and your table ID’s. Matt gives a great explanation in this post with a similar problem. feature ids much be present as tip names in phylogeny
As for the ID's, I checked the tree.nwk, the table.qza, the sample-metadata.tsv and all sample ids matched together, perhaps there is another file where I didn't check yet ?
Thanks again for your help !
Gabriel