---------------------------------------------------------------------------
LibraryError Traceback (most recent call last)
Cell In[60], line 1
----> 1 ts = msprime.sim_ancestry(
2 10,
3 #population_size=10,
4 stop_at_local_mrca=False,
5 end_time=1000,
6 random_seed=1,
7 sequence_length=10,
8 recombination_rate=0.01,
9 model=msprime.SmcKApproxCoalescent()
10 #model=msprime.SmcApproxCoalescent()
11 #model=msprime.BetaCoalescent(alpha=1.2)
12 #model='dtwf'
13 )
14 ts.draw_svg(y_axis=True)
File ~/Documents/msprime/msprime/ancestry.py:1332, in sim_ancestry(samples, demography, sequence_length, discrete_genome, recombination_rate, gene_conversion_rate, gene_conversion_tract_length, population_size, ploidy, model, initial_state, start_time, end_time, record_migrations, record_full_arg, additional_nodes, coalescing_segments_only, num_labels, random_seed, num_replicates, replicate_index, record_provenance, stop_at_local_mrca)
1309 provenance_dict = provenance.get_provenance_dict(parameters)
1310 sim = _parse_sim_ancestry(
1311 samples=samples,
1312 sequence_length=sequence_length,
(...) 1330 stop_at_local_mrca=stop_at_local_mrca,
1331 )
-> 1332 return _wrap_replicates(
1333 sim,
1334 num_replicates=num_replicates,
1335 replicate_index=replicate_index,
1336 provenance_dict=provenance_dict,
1337 )
File ~/Documents/msprime/msprime/ancestry.py:681, in _wrap_replicates(simulator, num_replicates, replicate_index, provenance_dict, mutation_rate)
675 iterator = simulator.run_replicates(
676 num_replicates,
677 mutation_rate=mutation_rate,
678 provenance_dict=provenance_dict,
679 )
680 if replicate_index is not None:
--> 681 deque = collections.deque(iterator, maxlen=1)
682 return deque.pop()
683 else:
File ~/Documents/msprime/msprime/ancestry.py:1629, in Simulator.run_replicates(self, num_replicates, mutation_rate, provenance_dict)
1627 for replicate_index in range(num_replicates):
1628 logger.info("Starting replicate %d", replicate_index)
-> 1629 self.run()
1630 if mutation_rate is not None:
1631 # This is only called from simulate() or the ms interface,
1632 # so does not need any further parameters.
1633 mutations._simple_mutate(
1634 tables=self.tables,
1635 random_generator=self.random_generator,
1636 sequence_length=self.sequence_length,
1637 rate=mutation_rate,
1638 )
File ~/Documents/msprime/msprime/ancestry.py:1594, in Simulator.run(self, event_chunk, debug_func)
1592 raise ValueError("Model durations must be >= 0")
1593 end_time = min(self.time + model_duration, self.end_time)
-> 1594 exit_reason = self._run_until(end_time, event_chunk, debug_func)
1595 if exit_reason == ExitReason.COALESCENCE or self.time == self.end_time:
1596 logger.debug("Skipping remaining %d models", len(self.models) - j - 1)
File ~/Documents/msprime/msprime/ancestry.py:1559, in Simulator._run_until(self, end_time, event_chunk, debug_func)
1557 ret = ExitReason.MAX_EVENTS
1558 while ret == ExitReason.MAX_EVENTS:
-> 1559 ret = ExitReason(super().run(end_time, event_chunk))
1560 if self.time > end_time:
1561 # Currently the Pedigree and Sweeps models are "non-reentrant"
1562 # We can change this to an assertion once these have been fixed.
1563 raise RuntimeError(
1564 f"Model {self.model['name']} does not support interruption. "
1565 "Please open an issue on GitHub"
1566 )
LibraryError: Infinite waiting time until next simulation event.
Simulating above the root, as implemented in #2396, causes infinite waiting time for smc modules when:
sample size =10, sequence_length=10, and recombination_rate=0.001,works with0hull offsetsample size =10, sequence_length=10, and recombination_rate>0.001,requires a+vehull offset (even a very small fraction)Error log: