Hi, about a month ago, I used the "qiime diversity core-metrics-phylogenetic" plugin on a feature table and successfully obtained results. Later, I noticed that one sample (ID: NT-55) was not displayed correctly in the PCoA plots, although this sample still exists in the feature table.
To understand why this sample point disappeared, I re-ran the command to generate the distance matrix. To my surprise, the newly generated plot was significantly different from the original one (I didn't make any modifications to the command line). I repeated this command three times, and the new results are highly consistent with each other.
I'm not sure what caused such significant differences or why you couldn't replicate the results from the first run (I used the
--quiet option, so I don't know what the output was when it ran). The three attachments are the files used for the analysis (feature table, metadata, and phylogeny tree), the results of the first diversity analysis, and the most recent analysis results.
featuretable_metadata_tree.zip (1.2 MB)
initial_core_metrics_results.zip (5.5 MB)
new-core-metrics-results.zip (3.2 MB)
Thank you in advance to anyone willing to help me.