rm -f ../opentree8.0/phylo_snapshot/stdouterr.txt
rm -f ../opentree8.0/phylo_snapshot/git_shas.txt ../opentree8.0/phylo_snapshot/collections_git_shas.txt ../opentree8.0/phylo_snapshot/concrete_rank_collection.json ../opentree8.0/phylo_input/rank_collection.json ../opentree8.0/phylo_input/collections.txt ../opentree8.0/phylo_input/study_tree_pairs.txt
find ../opentree8.0/phylo_snapshot/ -name "*.json" | xargs rm -f
rm -f ../opentree8.0/cleaned_ott/cleaned_ott.json ../opentree8.0/cleaned_ott/cleaned_ott_1.json ../opentree8.0/cleaned_ott/cleaned_ott_pruned_nonflagged.json ../opentree8.0/cleaned_ott/ott_version.txt ../opentree8.0/cleaned_ott/cleaned_ott_with_hiddenbarren.tre ../opentree8.0/cleaned_ott/cleaning_flags.txt
rm -f ../opentree8.0/cleaned_ott/cleaned_ott.tre
rm -f ../opentree8.0/cleaned_ott/root_ott_id.txt
rm -f ../opentree8.0/exemplified_phylo/nonempty_trees.txt ../opentree8.0/exemplified_phylo/taxonomy.tre ../opentree8.0/cleaned_phylo/cleaning_flags.txt ../opentree8.0/cleaned_phylo/root_ott_id.txt ../opentree8.0/cleaned_phylo/phylo_inputs_cleaned.txt ../opentree8.0/cleaned_phylo/needs_updating.txt ../opentree8.0/exemplified_phylo/args.txt ../opentree8.0/exemplified_phylo/exemplified_log.json ../opentree8.0/exemplified_phylo/pruned_taxonomy_degree_distribution.txt 
find ../opentree8.0/cleaned_phylo/ -name "*.tre" | xargs rm -f
find ../opentree8.0/cleaned_phylo/ -name "*.json" | xargs rm -f
find ../opentree8.0/exemplified_phylo/ -name "*.tre" | xargs rm -f
find ../opentree8.0/subproblems/scratch/ -name "*.tre" | xargs rm -f
find ../opentree8.0/subproblems/scratch/ -name "*.md5" | xargs rm -f
find ../opentree8.0/subproblems/scratch/ -name "*.txt" | xargs rm -f
find ../opentree8.0/subproblems/ -name "*.tre" | xargs rm -f
find ../opentree8.0/subproblems/ -name "*.md5" | xargs rm -f
find ../opentree8.0/subproblems/ -name "*.txt" | xargs rm -f
find ../opentree8.0/subproblem_solutions/ -name "*.tre" | xargs rm -f
rm -f ../opentree8.0/subproblems/subproblem-ids.txt ../opentree8.0/grafted_solution/grafted_solution.tre ../opentree8.0/grafted_solution/grafted_solution_ottnames.tre ../opentree8.0/subproblem_solutions/solution-ids.txt ../opentree8.0/subproblem_solutions/solution-degree-distributions.txt ../opentree8.0/subproblems/contesting-trees.json
rm -f ../opentree8.0/full_supertree/full_supertree.tre ../opentree8.0/labelled_supertree/broken_taxa.json ../opentree8.0/labelled_supertree/input_output_stats.json ../opentree8.0/labelled_supertree/labelled_supertree.tre ../opentree8.0/labelled_supertree/labelled_supertree_out_degree_distribution.txt ../opentree8.0/labelled_supertree/labelled_supertree_ottnames.tre ../opentree8.0/labelled_supertree/labelled_supertree_ottnames_without_monotypic.tre ../opentree8.0/labelled_supertree/labelled_supertree_simplified_ottnames.tre ../opentree8.0/labelled_supertree/labelled_supertree_simplified_ottnames_without_monotypic.tre ../opentree8.0/annotated_supertree/annotations.json ../opentree8.0/annotated_supertree/annotations1.json ../opentree8.0/annotated_supertree/annotations2.json
rm -f ../opentree8.0/labelled_supertree/simplified_ottnames.log
rm -f ../opentree8.0/labelled_supertree/simplified_ottnames_without_monotypic.log
rm -f ../opentree8.0/annotated_supertree/index.html ../opentree8.0/annotated_supertree/index.json ../opentree8.0/assessments/index.html ../opentree8.0/assessments/index.json ../opentree8.0/cleaned_ott/index.html ../opentree8.0/cleaned_ott/index.json ../opentree8.0/cleaned_phylo/index.json ../opentree8.0/cleaned_phylo/index.html ../opentree8.0/exemplified_phylo/index.html ../opentree8.0/exemplified_phylo/index.json ../opentree8.0/grafted_solution/index.html ../opentree8.0/grafted_solution/index.json ../opentree8.0/index.html ../opentree8.0/index.json ../opentree8.0/logs/index.html ../opentree8.0/logs/myeasylog.log ../opentree8.0/labelled_supertree/index.html ../opentree8.0/labelled_supertree/index.json ../opentree8.0/phylo_input/index.json ../opentree8.0/phylo_input/index.html ../opentree8.0/subproblems/index.html ../opentree8.0/subproblems/index.json ../opentree8.0/subproblem_solutions/index.html ../opentree8.0/subproblem_solutions/index.json ../opentree8.0/phylo_snapshot/index.html ../opentree8.0/phylo_snapshot/index.json
rm -f ../opentree8.0/README.md ../opentree8.0/labelled_supertree/README.md ../opentree8.0/grafted_solution/README.md ../opentree8.0/exemplified_phylo/README.md ../opentree8.0/phylo_input/README.md ../opentree8.0/logs/README.md ../opentree8.0/cleaned_phylo/README.md ../opentree8.0/subproblem_solutions/README.md ../opentree8.0/subproblems/README.md ../opentree8.0/subproblems/scratch/README.md ../opentree8.0/assessments/README.md ../opentree8.0/phylo_snapshot/README.md ../opentree8.0/annotated_supertree/README.md ../opentree8.0/cleaned_ott/README.md ../opentree8.0/logs/index.html
rm -f ../opentree8.0/assessments/supertree_degree_distribution.txt ../opentree8.0/assessments/taxonomy_degree_distribution.txt ../opentree8.0/assessments/lost_taxa.txt ../opentree8.0/assessments/summary.json ../opentree8.0/assessments/log.txt
rmdir ../opentree8.0/phylo_input || true
rmdir ../opentree8.0/phylo_snapshot || true
rmdir ../opentree8.0/cleaned_ott || true
rmdir ../opentree8.0/cleaned_phylo || true
rmdir ../opentree8.0/exemplified_phylo || true
rmdir ../opentree8.0/subproblems/scratch || true
rmdir ../opentree8.0/subproblems || true
rmdir ../opentree8.0/subproblem_solutions || true
rmdir ../opentree8.0/grafted_solution || true
rmdir ../opentree8.0/labelled_supertree || true
rmdir ../opentree8.0/annotated_supertree || true
rmdir ../opentree8.0/logs || true
# if test -d ../opentree8.0/phylo_input ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/phylo_input ; fi
# if test -d ../opentree8.0/phylo_snapshot ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/phylo_snapshot ; fi
# if test -d ../opentree8.0/cleaned_ott ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/cleaned_ott ; fi
# if test -d ../opentree8.0/cleaned_phylo ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/cleaned_phylo ; fi
# if test -d ../opentree8.0/exemplified_phylo ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/exemplified_phylo ; fi
# if test -d ../opentree8.0/subproblems/scratch ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/subproblems/scratch ; fi
# if test -d ../opentree8.0/subproblems ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/subproblems ; fi
# if test -d ../opentree8.0/subproblem_solutions ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/subproblem_solutions ; fi
# if test -d ../opentree8.0/grafted_solution ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/grafted_solution ; fi
# if test -d ../opentree8.0/labelled_supertree ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/labelled_supertree ; fi
# if test -d ../opentree8.0/annotated_supertree ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/annotated_supertree ; fi
# if test -d ../opentree8.0/assessments ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/assessments ; fi
# if test -d ../opentree8.0/logs ; then rmdir --ignore-fail-on-non-empty ../opentree8.0/logs ; fi