cat /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/nonempty_trees.txt \
	| sed -e "s:^:/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/:g" \
	> /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/scratch/args.txt
./bin/run-subproblem-finder.sh \
	  /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/scratch \
	  /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/dumped-subproblem-ids.txt \
	  /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/contesting-trees.json \
	  /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/taxonomy.tre \
	  -f/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/scratch/args.txt
bash bin/checksum-tree-files.sh \
		/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/scratch \
	&& \
		cp /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/dumped-subproblem-ids.txt \
		   /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/checksummed-subproblem-ids.txt
/Users/karen/Documents/opentreeoflife/software/propinquity-clean
bash bin/move-subproblem-if-differing.sh \
		/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/scratch \
		/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems \
		/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/checksummed-subproblem-ids.txt \
	&& \
		cp /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/checksummed-subproblem-ids.txt \
		   /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/subproblem-ids.txt
otc-taxonomy-parser --config=/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/config \
	  	--in-tree=/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/taxonomy.tre \
		--any-flag=incertae_sedis,major_rank_conflict,unplaced,unclassified \
		--format="%I" \
		> /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/incertae_sedis.txt
for n in $(cat /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/subproblem-ids.txt) ; do \
		id=${n%.tre} ; \
		otc-solve-subproblem \
			/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/$n \
			-n${id} \
			-I /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/incertae_sedis.txt \
			> /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblem_solutions/${n} ; \
	done ;
cp /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblems/subproblem-ids.txt \
	   /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblem_solutions/solution-ids.txt
sed "s:^:/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblem_solutions/:" \
		/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblem_solutions/solution-ids.txt \
		> /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblem_solutions/paths.txt
otc-graft-solutions -f/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblem_solutions/paths.txt \
		> /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/grafted_solution/.grafted_solution.tre && \
	mv /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/grafted_solution/.grafted_solution.tre \
	   /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/grafted_solution/grafted_solution.tre
rm /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/subproblem_solutions/paths.txt
otc-unprune-solution-and-name-unnamed-nodes \
		/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/grafted_solution/grafted_solution.tre \
		/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/cleaned_ott/cleaned_ott.tre \
		-i/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/exemplified_phylo/incertae_sedis.txt \
		-j/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/labelled_supertree/broken_taxa.json \
		-s/Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/labelled_supertree/input_output_stats.json \
		> /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/labelled_supertree/labelled_supertree.tre