otc-degree-distribution /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/cleaned_ott/cleaned_ott.tre > /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/assessments/taxonomy_degree_distribution.txt otc-degree-distribution \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/labelled_supertree/labelled_supertree.tre \ > /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/assessments/supertree_degree_distribution.txt otc-taxonomy-parser \ $(./bin/config_checker.py opentree.ott /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/config ) \ --report-lost-taxa \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/labelled_supertree/labelled_supertree.tre \ -c /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/config > /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/assessments/.lost_taxa.txt \ || rm /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/assessments/.lost_taxa.txt mv /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/assessments/.lost_taxa.txt /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/assessments/lost_taxa.txt ./bin/combine_ott_cleaning_logs.py \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/cleaned_ott/cleaned_ott_1.json \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/cleaned_ott/cleaned_ott_pruned_nonflagged.json \ /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/cleaned_ott/cleaned_ott.json ./bin/run_assessments.py /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1 /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/assessments/summary.json 2>&1 | tee /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.1/assessments/log.txt || true