Hi @ruby --- that error message is actually saying that the command qiime diversity core-metrics-phylogenetic doesn't have a --m-metadata-file option, not that it can't find your metadata file. It looks like you are running QIIME 2 2017.9, but are referencing the docs for QIIME 2 2017.12. We added the option to provide metadata to this pipeline in 2017.10, which is why you are seeing this particular error.
You have two options - upgrade to QIIME 2 2017.12 (personally I would go with this option), or, use the dropdown on the docs site to pick 2017.9 as the version of the docs to reference. Hope that helps! 