Propinquity output documentation. The top-level docs are here.
This directory holds the output of
a run of propinquity's run_assessments.py script.
That script checks for certain types of problems in the output of the pipeline.
summary.json is a JSON representation of that data
and log.txt is a text log of the assessments run
(the text log will be empty if there are no errors).
The 5 checks run were:
| nickname of check | description |
|---|---|
lost_taxa |
Check that otcetera's tc-taxonomy-parser and otc-unprune-solution-and-name-unnamed-nodes tools agree about the number of taxa that are not present in the solution |
lost_taxa_included_in_tree |
Check that none of the taxa listed as "lost" are in the annotations file |
monophyly |
Check that the taxa from the monophyly tests listed in https://github.com/OpenTreeOfLife/germinator/blob/master/taxa/monophyly.csv are monophyletic in the tree. |
num_tips |
Check that the cleaned version of the taxonomy and the supertree have the same number of leaves |
unsupported_nodes |
Check that none of the nodes listed in the annotations file are completely unsuported |
SUCCESS! No errors were found.