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 checkdescription
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.