otc-degree-distribution /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/exemplified_phylo/regraft_cleaned_ott.tre > /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/assessments/taxonomy_degree_distribution.txt otc-degree-distribution \ /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/labelled_supertree/labelled_supertree.tre \ > /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/assessments/supertree_degree_distribution.txt otc-tree-tool \ /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/labelled_supertree/labelled_supertree.tre \ --lost-taxa-vs=/home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/exemplified_phylo/regraft_cleaned_ott.tre \ --taxonomy=/home/opentree/synth/ott/ott3.2.0-bumped-tree-12.3 \ > /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/assessments/.lost_taxa.txt \ || rm /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/assessments/.lost_taxa.txt mv /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/assessments/.lost_taxa.txt /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/assessments/lost_taxa.txt ./bin/combine_ott_cleaning_logs.py \ /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/cleaned_ott/cleaned_ott_1.json \ /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/cleaned_ott/cleaned_ott_pruned_nonflagged.json \ /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/cleaned_ott/cleaned_ott.json ./bin/run_assessments.py /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3 /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/assessments/summary.json 2>&1 | tee /home/opentree/synth/in_progress_tree_builds/bumpedopentree12.3/assessments/log.txt || true MONOPHYLY_TEST_CSV_FILE is not in the env, so no monophyly tests are being run