cat ../opentree8.0/exemplified_phylo/nonempty_trees.txt \
	| sed -e "s:^:../opentree8.0/exemplified_phylo/:g" \
	> ../opentree8.0/subproblems/scratch/args.txt
./bin/run-subproblem-finder.sh \
	  ../opentree8.0/subproblems/scratch \
	  ../opentree8.0/subproblems/dumped-subproblem-ids.txt \
	  ../opentree8.0/subproblems/contesting-trees.json \
	  ../opentree8.0/exemplified_phylo/taxonomy.tre \
	  -f../opentree8.0/subproblems/scratch/args.txt
bash bin/checksum-tree-files.sh \
		../opentree8.0/subproblems/scratch \
	&& \
		cp ../opentree8.0/subproblems/dumped-subproblem-ids.txt \
		   ../opentree8.0/subproblems/checksummed-subproblem-ids.txt
/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/propinquity
bash bin/move-subproblem-if-differing.sh \
		../opentree8.0/subproblems/scratch \
		../opentree8.0/subproblems \
		../opentree8.0/subproblems/checksummed-subproblem-ids.txt \
	&& \
		cp ../opentree8.0/subproblems/checksummed-subproblem-ids.txt \
		   ../opentree8.0/subproblems/subproblem-ids.txt
for n in $(cat ../opentree8.0/subproblems/subproblem-ids.txt) ; do \
		id=${n%.tre} ; \
		otc-solve-subproblem \
			../opentree8.0/subproblems/$n \
			-n${id} \
			> ../opentree8.0/subproblem_solutions/${n} ; \
	done ;
cp ../opentree8.0/subproblems/subproblem-ids.txt \
	   ../opentree8.0/subproblem_solutions/solution-ids.txt
sed "s:^:../opentree8.0/subproblem_solutions/:" \
		../opentree8.0/subproblem_solutions/solution-ids.txt \
		> ../opentree8.0/subproblem_solutions/paths.txt
otc-graft-solutions -f../opentree8.0/subproblem_solutions/paths.txt \
		> ../opentree8.0/grafted_solution/.grafted_solution.tre && \
	mv ../opentree8.0/grafted_solution/.grafted_solution.tre \
	   ../opentree8.0/grafted_solution/grafted_solution.tre
rm ../opentree8.0/subproblem_solutions/paths.txt
otc-unprune-solution-and-name-unnamed-nodes \
		../opentree8.0/grafted_solution/grafted_solution.tre \
		../opentree8.0/cleaned_ott/cleaned_ott.tre \
		-j../opentree8.0/labelled_supertree/broken_taxa.json \
		-s../opentree8.0/labelled_supertree/input_output_stats.json \
		> ../opentree8.0/labelled_supertree/labelled_supertree.tre