The taxonomic profile for each sample will be located under the temp/ folder of a HUMAnN run, and it will be available before other files (e.g. genefamilies.tsv) finish. Another option is to run MetaPhlAn on the samples outside of HUMAnN to build your table. You can then pass a pre-existing taxonomic profile for a sample to HUMAnN (so it skips that step) using the --taxonomic-profile flag.