Failure to load dropped Newick file #71
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bug
Something isn't working
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Thanks for the bug report! I don't have the time to fix this right at the moment but hopefully someone on the team can. The tree parsing fails because of This error was introduced ~a month ago by #69 |
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Thank you so much for the quick answer @jameshadfield! |
jameshadfield
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Dec 6, 2023
Two recent issues (#71, #72) provide examples where the improved parsing either didn't parse a valid newick tree or (much more worryingly) returned an entirely incorrect tree structure, including nodes not present in the newick. See those issues for details, including the tree files. While this reversion will re-introduce bugs such as #66 and the bug in <https://discussion.nextstrain.org/t/displaying-trees-from-ncbi-pathogen-browser-in-auspice-us/1456/4>, but they are lesser than the bugs introduced by #69. This reverts commit cabba98, although subsequent changes to package-lock.json mean it's not a clean revert.
jameshadfield
added a commit
that referenced
this issue
Dec 6, 2023
Two recent issues (#71, #72) provide examples where the improved parsing either didn't parse a valid newick tree or (much more worryingly) returned an entirely incorrect tree structure, including nodes not present in the newick. See those issues for details, including the tree files. While this reversion will re-introduce bugs such as #66 and the bug in <https://discussion.nextstrain.org/t/displaying-trees-from-ncbi-pathogen-browser-in-auspice-us/1456/4>, but they are lesser than the bugs introduced by #69. This reverts commit cabba98, although subsequent changes to package-lock.json mean it's not a clean revert.
jameshadfield
added a commit
that referenced
this issue
Dec 6, 2023
Two recent issues (#71, #72) provide examples where the improved parsing either didn't parse a valid newick tree or (much more worryingly) returned an entirely incorrect tree structure, including nodes not present in the newick. See those issues for details, including the tree files. While this reversion will re-introduce bugs such as #66 and the bug in <https://discussion.nextstrain.org/t/displaying-trees-from-ncbi-pathogen-browser-in-auspice-us/1456/4>, but they are lesser than the bugs introduced by #69. This reverts commit cabba98, although subsequent changes to package-lock.json mean it's not a clean revert.
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This tree should now be correctly displayed in auspice.us (via #73) |
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Current Behavior
Hello, I am trying to load the attached Newick file in auspice.us, but am seeing the failure to load error shown below. (I am attempting to load the file with the file ending .nwk, but was not able to link that file time to this GitHub issue so have attached it as .txt instead.)
test_tree_20231205.txt
How to reproduce
Steps to reproduce the current behavior:
Your environment: if browsing Nextstrain online
Additional context
Tree was generated using the Snippy_Tree_PHB workflow on Terra and was successfully loaded in other tree visualization tools including iTol and MicroReact.
The text was updated successfully, but these errors were encountered: