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pbradleylab / phylogenize

A tool for phylogenetic comparison and analysis of microbe including gene's environmental association
https://phylogenize.org/
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Species being all filtered out for tree min #17

Open Kekananen opened 2 months ago

Kekananen commented 2 months ago

When running on 16S data with prevalence and gtdb selected. Runs fine with UHGP

Quitting from lines 40-100 [setup] (phylogenize-report.Rmd) Error in pz.error(): ! All trees had less than 2.5% of species observed. Either a very small ASV table was provided, read depth was very shallow, the right database was not selected or very few ASVs mapped to entries in the database. Backtrace:

  1. phylogenize::adjust.db(pz.db, abd.meta)
  2. phylogenize::pz.error(...) at phylogenize/R/report-functions.R:886:9 Execution halted
Kekananen commented 2 months ago

No values are passing passed.pct <- nw(pct.obs >= opts('pctmin'))

Kekananen commented 2 months ago

Okay fixed the tree file which has some duplicate labels (string and integer). This still did not fix the issue however, was good to fix regardless.