`IndexError: index 0 is out of bounds for axis 0 with size 0` in `--use-fft` mode about treetime HOT 3 CLOSED

$ 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 0.9.6

71.35   WARNING: Previous versions of TreeTime (<0.7.0) RECONSTRUCTED sequences of
        tips at positions with AMBIGUOUS bases. This resulted in unexpected
        behavior is some cases and is no longer done by default. If you want to
        replace those ambiguous sites with their most likely state, rerun with
        `reconstruct_tip_states=True` or `--reconstruct-tip-states`.

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

254.55  ###TreeTime.run: INITIAL ROUND

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

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

320.28  ###TreeTime.run: ITERATION 1 out of 2 iterations
Warning: evaluating log probability of a delta distribution.

366.03  ###TreeTime.run: ITERATION 2 out of 2 iterations
Warning: evaluating log probability of a delta distribution.
Warning: evaluating log probability of a delta distribution.
Warning: evaluating log probability of a delta distribution.
Warning: evaluating log probability of a delta distribution.

Inferred a time resolved phylogeny using TreeTime:
        Sagulenko et al. TreeTime: Maximum-likelihood phylodynamic analysis
        Virus Evolution, vol 4, https://academic.oup.com/ve/article/4/1/vex042/4794731

updated tree written to results/hmpxv1/tree.nwk
node attributes written to results/hmpxv1/branch_lengths.json