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BUG: Refine fails with A value in x_new is above the interpolation range. #1032

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corneliusroemer opened this issue Aug 22, 2022 · 2 comments · May be fixed by neherlab/treetime#205
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BUG: Refine fails with A value in x_new is above the interpolation range. #1032

corneliusroemer opened this issue Aug 22, 2022 · 2 comments · May be fixed by neherlab/treetime#205
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@rneher @anna-parker
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bug Something isn't working treetime Upstream issue with treetime

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@corneliusroemer
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I've encountered the following bug twice in monkeypox CI running in Github Actions:

ERROR: Was unable to refine time trees:
augur refine is using TreeTime version 0.9.2

A value in x_new is above the interpolation range.

This error seems to be somewhat stochastic, i.e. if I rerun, it will often run successfully after bug.

This seems to be related to the upgrade of tree time from 0.8.6 to 0.9.2 @anna-parker @rneher

See here for log: https://github.com/nextstrain/monkeypox/runs/7955938588?check_suite_focus=true#step:6:177

Not sure how to reproduce - maybe run the monkeypox CI a few times locally until you get the error?
@corneliusroemer corneliusroemer added bug Something isn't working treetime Upstream issue with treetime labels Aug 22, 2022
@corneliusroemer corneliusroemer moved this from New to Prioritized in Nextstrain planning (archived) Aug 22, 2022
@anna-parker anna-parker mentioned this issue Aug 22, 2022
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@corneliusroemer
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corneliusroemer commented Aug 29, 2022 •
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Hah, we hit the error again and now we have the builds files from CI @anna-parker
https://github.com/nextstrain/monkeypox/runs/8060259099?check_suite_focus=true#step:6:178

It ran in this Docker container: Digest: sha256:2c6b71c463de7fe7a0277f24471b46515c0106d6ffbf28e4381ba5a829671dd9

With this command:
augur refine --tree results/hmpxv1/tree_raw.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 --output-node-data results/hmpxv1/branch_lengths.json --coalescent opt --date-inference marginal --date-confidence --clock-filter-iqd 0

These are the build files
results.zip

@corneliusroemer
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This time it really seems reproducible - happened again on rerun.
https://github.com/nextstrain/monkeypox/runs/8060259099?check_suite_focus=true#step:6:178

@anna-parker anna-parker mentioned this issue Aug 29, 2022
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@rneher rneher mentioned this issue Aug 29, 2022
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@anna-parker anna-parker mentioned this issue Sep 2, 2022
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@rneher rneher closed this as completed Sep 21, 2022
Repository owner moved this from Prioritized to Done in Nextstrain planning (archived) Sep 21, 2022
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bug Something isn't working treetime Upstream issue with treetime
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New upper bound for inter1d objects neherlab/treetime
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@rneher @corneliusroemer @anna-parker