❯ augur refine --tree results/hmpxv1/tree_fixed.nwk --alignment results/hmpxv1/masked.fasta --metadata results/hmpxv1/metadata.tsv --output-tree results/hmpxv1/tree.nwk --timetree --root MK783032 MK783030 --precision 3 --keep-polytomies --clock-rate 5.7e-05 --clock-std-dev 2e-5 --use-fft --output-node-data results/hmpxv1/branch_lengths.json --coalescent opt --date-inference marginal --date-confidence --clock-filter-iqd 0

augur refine is using TreeTime version 0.10.0

191.21  TreeTime.reroot: with method or node: ['MK783032', 'MK783030']

258.67  ###TreeTime.run: INITIAL ROUND

272.38  TreeTime.reroot: with method or node: ['MK783032', 'MK783030']

274.37  ###TreeTime.run: rerunning timetree after rerooting

322.01  ###TreeTime.run: ITERATION 1 out of 2 iterations

367.97  ###TreeTime.run: ITERATION 2 out of 2 iterations
Traceback (most recent call last):
  File "/opt/homebrew/Caskroom/miniforge/base/envs/py11/lib/python3.11/site-packages/treetime/treetime.py", line 57, in run
    return self._run(**kwargs)
           ^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Caskroom/miniforge/base/envs/py11/lib/python3.11/site-packages/treetime/treetime.py", line 330, in _run
    self.calc_rate_susceptibility(rate_std=vary_rate, params=tt_kwargs)
  File "/opt/homebrew/Caskroom/miniforge/base/envs/py11/lib/python3.11/site-packages/treetime/clock_tree.py", line 874, in calc_rate_susceptibility
    self.make_time_tree(**params)
  File "/opt/homebrew/Caskroom/miniforge/base/envs/py11/lib/python3.11/site-packages/treetime/clock_tree.py", line 374, in make_time_tree
    self._ml_t_marginal()
  File "/opt/homebrew/Caskroom/miniforge/base/envs/py11/lib/python3.11/site-packages/treetime/clock_tree.py", line 732, in _ml_t_marginal
    res, res_t = NodeInterpolator.convolve_fft(msg_parent_to_node, node.branch_length_interpolator,
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Caskroom/miniforge/base/envs/py11/lib/python3.11/site-packages/treetime/node_interpolator.py", line 234, in convolve_fft
    if Tmin<Tres_cropped[0] and left_slope<0:
            ~~~~~~~~~~~~^^^
IndexError: index 0 is out of bounds for axis 0 with size 0

curl -L -o hmpxv1_fft_treetime_bug.tar.zst  https://github.com/neherlab/treetime/files/11530736/hmpxv1_fft_treetime_bug.tar.zst.txt
unzstd hmpxv1_fft_treetime_bug.tar.zst 
augur refine --tree results/hmpxv1/tree_fixed.nwk --alignment results/hmpxv1/masked.fasta --metadata results/hmpxv1/metadata.tsv --output-tree results/hmpxv1/tree.nwk --timetree --root MK783032 MK783030 --precision 3 --keep-polytomies --clock-rate 5.7e-05 --clock-std-dev 2e-5 --use-fft --output-node-data results/hmpxv1/branch_lengths.json --coalescent opt --date-inference marginal --date-confidence --clock-filter-iqd 0