Filled by make's use of the:
otc-uncontested-decompose -estep_7_scratch/export-sub-temp step_6/taxonomy.tre -fstep_7/step-7-phylo-args.txt
command where step_7/step-7-phylo-args.txt is the filename of each tree with the step_5/ prefix
added to it.
If that succeeds, make will also invoke:
bash checksum-tree-files.sh step_7_scratch/export-sub-temp
Subproblems are written in the export-sub-temp directory here.
dumped-subproblem-ids.txt will be written if the decompostition
succeeds. It contains the tree filenames of the subproblems trees (just their names, not their paths).
If that succeeds, then each subproblem is check summed with md5.
If that also succeeds, then checksummed-subproblem-ids.txt will be created.
It is just a copy of dumped-subproblem-ids.txt that serves as a sentinel for the successful
execution of the checksum.
The otc-uncontested-decompose invocation produces a subproblem
file of newicks (called ott123.tre if the OTT Id was "123")
for each uncontested taxon and a file of tree names.
The file of names will be called ott123-tree-names.txt if the
uncontested taxon was OTT 123.
This file will have a line for each newick in the .tre file.
Each line will hold either tree file name for each phylo tree that contributed
to the subproblem or the word "TAXONOMY" if the tree is from the taxonomy.
The taxonomy is always last, and the order of the other trees is determined
by their order of input.
That is determined ultimately, but the order of the tree identifiers in
step_1/tree-ranking.txt, so the order in the subproblems reflects the tree rankings.
The checksum-tree-files.sh step create the ott###.md5 files.
These will be used to quickly determine if a subproblem has changed
from the previous invocation.
The idea is that the tree files will be moved to their their final location
(the step_7 subdirectory) only if they differ from content there
(based on diffing their checksums).
This should enable caching of solutions to subproblems.