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

The cleaned_ott directory contains the results of pruning OTT version 3.3draft1 so that the root is 93302 and the taxa flagged with the following flags were removed:

• barren
• environmental
• hidden
• hybrid
• inconsistent
• major_rank_conflict
• major_rank_conflict_inherited
• merged
• not_otu
• viral
• was_container

Next step: Bump extinct taxa higher in the taxonomy, if necessary so that moving an extinct taxon does not disrupt the phylogenetic naming later in the pipeline. ../bumped_ott/index.html.

Results:

• cleaning_flags.txt holds the flags that signal that taxon shoule be pruned from the taaxonomy before synthesis (this is one aspect of the configuration, serialized here for convenience).
• cleaned_ott.json is a JSON summary (often a large file that can be hard to look at in a browser) that lists the reasons different taxa were pruned. The file is composed from 3 different files (which are rarely of direct interest to end-users): flagged_in_cleaned.json, cleaned_ott_pruned_nonflagged.json, and cleaned_ott_1.json. The following table summarizes the information in cleaned_ott.json by showing the number of OTT IDs pruned by the combination of flags that caused the pruning (we don't list each of the OTT ID here because the list is extremely long and can make your browser hang.):

  Combination of flags	# of nodes pruned
  barren	1
  barren,hidden	2
  barren,hidden,inconsistent	1
  barren,hidden,inconsistent,major_rank_conflict	1
  barren,hidden,major_rank_conflict	29
  barren,hidden,major_rank_conflict,merged	4
  barren,hidden,merged	4
  barren,hidden,was_container	8
  barren,hybrid	2
  barren,inconsistent	18
  barren,inconsistent,major_rank_conflict	2
  barren,major_rank_conflict	11
  barren,major_rank_conflict,merged	1
  barren,merged	3
  barren,not_otu,was_container	8
  barren,was_container	1
  empty-after-higher-taxon-tip-prune	30
  environmental	2
  environmental,hidden	73
  environmental,hidden,not_otu	25
  environmental,inconsistent	14
  environmental,inconsistent,not_otu	9
  environmental,merged	2
  environmental,merged,not_otu	2
  environmental,not_otu	36
  environmental,not_otu,was_container	1
  hidden	11
  hidden,inconsistent	8
  hidden,major_rank_conflict	13
  hidden,merged	2
  hidden,not_otu	6
  hidden,was_container	8
  higher-taxon-tip	1,904
  hybrid	1
  hybrid,not_otu	2
  hybrid,not_otu,was_container	1
  inconsistent	30
  inconsistent,not_otu	1
  major_rank_conflict	2
  major_rank_conflict,merged	2
  merged	1
  merged,not_otu	1
  not_otu	9
  not_otu,viral	3
  not_otu,was_container	1
  was_container	4

• cleaned_not_updated_ott.tre is a newick representation of the taxonomy with a total of 3,943,129 nodes. 3,676,616 of these are leaves and 266,513 internal nodes.
• cleaned_ott_with_hiddenbarren.tre is another representation of the taxonomic tree. This file contains higher taxa that lack descendants. Such taxa are pruned from the cleaned_not_updated_ott.tre form.
• move_extinct_higher_log.json is a file that summarizes a check of whether or not some of the extinct taxa should be moved rootward (higher) in the taxonomy. If their is an "edits" property in this file, then the ../bumped_ott directory will hold a modified version of the taxonomy.
• ott_version.txt holds the ID for the canonical OTT version used as an input to the synthesis
• root_ott_id.txt holds the root OTT ID (copy of info in other directories just for convenience).