Propinquity output documentation. The top-level docs are here.

This directory holds the output of a run of propinquity's 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 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.