BUG(refine): With `--use-fft`, refine occasionally fails with `ERROR: No module named 'ipdb'`

[corneliusroemer]

Current Behavior

When running refine on the monkeypox builds hmpxv1 and hmpxv1_big we quite often get a failure with ERROR: No module named 'ipdb'

Expected behavior

No failure of refine.

Workaround

Remove --use-fft flag for the time being

This is probably an upstream treetime bug but I'll still open it here in case other users have the same issue.

Example log:

[batch] [2022-10-03T01:23:22+02:00]         Refining tree
[batch] [2022-10-03T01:23:22+02:00]           - estimate timetree
[batch] [2022-10-03T01:23:22+02:00]           - use opt coalescent timescale
[batch] [2022-10-03T01:23:22+02:00]           - estimate marginal node dates
[batch] [2022-10-03T01:23:22+02:00]           - filter tips more than 0 IQDs from clock expectation
[batch] [2022-10-03T01:23:22+02:00]         
[batch] [2022-10-03T01:23:22+02:00]         augur refine             --tree results/hmpxv1_big/tree_fixed.nwk             --alignment results/hmpxv1_big/masked.fasta             --metadata results/hmpxv1_big/metadata.tsv             --output-tree results/hmpxv1_big/tree.nwk             --timetree             --use-fft             --root MK783032 MK783030             --precision 3             --keep-polytomies             --clock-rate 5.7e-05             --clock-std-dev 2e-5             --use-fft             --output-node-data results/hmpxv1_big/branch_lengths.json             --coalescent opt             --date-inference marginal             --date-confidence             --clock-filter-iqd 0
[batch] [2022-10-03T01:23:22+02:00]         
[batch] [2022-10-03T01:40:41+02:00] Traceback (most recent call last):
[batch] [2022-10-03T01:40:41+02:00]   File "/usr/local/lib/python3.7/site-packages/treetime/treetime.py", line 57, in run
[batch] [2022-10-03T01:40:41+02:00]     return self._run(**kwargs)
[batch] [2022-10-03T01:40:41+02:00]   File "/usr/local/lib/python3.7/site-packages/treetime/treetime.py", line 295, in _run
[batch] [2022-10-03T01:40:41+02:00]     self.make_time_tree(**tt_kwargs)
[batch] [2022-10-03T01:40:41+02:00]   File "/usr/local/lib/python3.7/site-packages/treetime/clock_tree.py", line 378, in make_time_tree
[batch] [2022-10-03T01:40:41+02:00]     self._ml_t_marginal()
[batch] [2022-10-03T01:40:41+02:00]   File "/usr/local/lib/python3.7/site-packages/treetime/clock_tree.py", line 728, in _ml_t_marginal
[batch] [2022-10-03T01:40:41+02:00]     fft_grid_size = self.fft_grid_size, inverse_time=False), None
[batch] [2022-10-03T01:40:41+02:00]   File "/usr/local/lib/python3.7/site-packages/treetime/node_interpolator.py", line 202, in convolve_fft
[batch] [2022-10-03T01:40:41+02:00]     import ipdb; ipdb.set_trace()
[batch] [2022-10-03T01:40:41+02:00] ModuleNotFoundError: No module named 'ipdb'
[batch] [2022-10-03T01:40:41+02:00] augur refine is using TreeTime version 0.9.4
[batch] [2022-10-03T01:40:41+02:00] ERROR: No module named 'ipdb' 
[batch] [2022-10-03T01:40:41+02:00]  
[batch] [2022-10-03T01:40:41+02:00] ERROR in TreeTime.run: An error occurred which was not properly handled in TreeTime. If this error persists, please let us know by filing a new issue including the original command and the error above at: https://github.com/neherlab/treetime/issues 
[batch] [2022-10-03T01:40:41+02:00] 229.45      WARNING: Previous versions of TreeTime (<0.7.0) RECONSTRUCTED sequences
[batch] [2022-10-03T01:40:41+02:00] ERROR from TreeTime: An error occurred in TreeTime (see above). This may be due to an issue with TreeTime or Augur.