cat ../opentree5.0/exemplified_phylo/nonempty_trees.txt \
| sed -e "s:^:../opentree5.0/exemplified_phylo/:g" \
> ../opentree5.0/subproblems/scratch/args.txt
./bin/run-subproblem-finder.sh \
  ../opentree5.0/subproblems/scratch \
  ../dumped-subproblem-ids.txt \
  ../opentree5.0/exemplified_phylo/taxonomy.tre \
  -f../opentree5.0/subproblems/scratch/args.txt
bash bin/checksum-tree-files.sh \
	../opentree5.0/subproblems/scratch \
&& \
	cp ../opentree5.0/subproblems/dumped-subproblem-ids.txt \
	   ../opentree5.0/subproblems/checksummed-subproblem-ids.txt
/home/mholder/Documents/projects/ot/full-propinquity
bash bin/move-subproblem-if-differing.sh \
	../opentree5.0/subproblems/scratch \
	../opentree5.0/subproblems \
	../opentree5.0/subproblems/checksummed-subproblem-ids.txt \
&& \
	cp ../opentree5.0/subproblems/checksummed-subproblem-ids.txt \
	   ../opentree5.0/subproblems/subproblem-ids.txt
for n in $(cat ../opentree5.0/subproblems/subproblem-ids.txt) ; do \
	id=${n%.tre} ; \
	otc-solve-subproblem \
		../opentree5.0/subproblems/$n \
		-n${id} \
		> ../opentree5.0/subproblem_solutions/${n} ; \
done ;
cp ../opentree5.0/subproblems/subproblem-ids.txt \
   ../opentree5.0/subproblem_solutions/solution-ids.txt
sed "s:^:../opentree5.0/subproblem_solutions/:" \
	../opentree5.0/subproblem_solutions/solution-ids.txt \
	> ../opentree5.0/subproblem_solutions/paths.txt
otc-graft-solutions $(cat ../opentree5.0/subproblem_solutions/paths.txt) \
	> ../opentree5.0/grafted_solution/.grafted_solution.tre && \
mv ../opentree5.0/grafted_solution/.grafted_solution.tre \
   ../opentree5.0/grafted_solution/grafted_solution.tre
rm ../opentree5.0/subproblem_solutions/paths.txt
otc-unprune-solution-and-name-unnamed-nodes \
	../opentree5.0/grafted_solution/grafted_solution.tre \
	../opentree5.0/cleaned_ott/cleaned_ott.tre \
	-j../opentree5.0/labelled_supertree/broken_taxa.json \
	-s../opentree5.0/labelled_supertree/input_output_stats.json \
	> ../opentree5.0/labelled_supertree/labelled_supertree.tre