diff --git a/treetime/treetime.py b/treetime/treetime.py index 669036d5..078fddfc 100644 --- a/treetime/treetime.py +++ b/treetime/treetime.py @@ -73,7 +73,7 @@ def run(self, raise_uncaught_exceptions=False, **kwargs): sys.exit(2) - def _run(self, root=None, infer_gtr=True, relaxed_clock=None, clock_filter_method='residuals', + def _run(self, root=None, infer_gtr=True, relaxed_clock=None, clock_filter_method='residual', n_iqd = None, resolve_polytomies=True, max_iter=0, Tc=None, fixed_clock_rate=None, time_marginal='never', sequence_marginal=False, branch_length_mode='auto', vary_rate=False, use_covariation=False, tracelog_file=None, @@ -423,6 +423,8 @@ def clock_filter(self, reroot='least-squares', method='residual', bad_branch_count = residual_filter(self, n_iqd) elif method=='local': bad_branch_count = local_filter(self, n_iqd) + else: + raise ValueError(f"TreeTime.clock_filter: unknown clock-filter method '{method}'. Implemented methods are: 'residual', 'local'") if bad_branch_count>0.34*self.tree.count_terminals(): self.logger("TreeTime.clock_filter: More than a third of leaves have been excluded by the clock filter. Please check your input data.", 0, warn=True)