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