so I got this after running the command:
(qiime2-2017.7) mpbair:~ mpb$ qiime diversity core-metrics --i-phylogeny /rooted-tree.qza --i-table /otu.table2.silva.filtered.qza --p-sampling-depth 7500 --output-dir /core-metrics-results Plugin error from diversity: All ``feature_ids`` must be present as tip names in ``phylogeny``. ``feature_ids`` not corresponding to tip names (n=1923): Otu1386 Otu373 Otu1585 Otu285 Otu1805 Otu2030 Otu1818 Otu1159........
So, the biom table was imported from a qiime1-generated bio file, with no errors. I did a back-export from the .qza to a boom file an then to tab file and the many Otus listed in the error look fine in the table. To generate the tree I actually used qiime2, I imported the fasta file of the OTUs, (I looked dat the headers and are identical to those in the table), did the alignment, masking, unrooted then rooted tree according to the scripts in the tutorial, with no errors. I feels its something to do with the import from the qiime1 boom table (what else could it be?), but I can’t find any differences in the sequence names, and the error refers to n=1923, there are about 2500 OTUs, so some are fine? Thank you in advance for any suggestions!