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yatisht / usher

Ultrafast Sample Placement on Existing Trees
MIT License
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`Warning/Error(s): Missing file subtree-1-mutations.txt in usher results` when uploading mpox sequences #330

Open corneliusroemer opened 1 year ago

corneliusroemer commented 1 year ago

When uploading around 80 mpox sequences (16MB) to Usher (both production and dev), I get the following error:

Warning/Error(s):
Missing file subtree-1-mutations.txt in usher results
Warning: multiple alignments found for sequence hMpxV/USA/CA-LACPHL-MA00425/2022|EPI_ISL_16997452|2022-12-03 (0-195592 and 178339-178407). Skipping alignment of 178339-178407
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These are the settings I use:

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AngieHinrichs commented 1 year ago

Sorry about that and thanks for the report! Taking a look...

AngieHinrichs commented 1 year ago

The requested subtree size (5000) being greater than the number of samples in the current tree (3741) is causing a SEGV in usher-sampled. @yceh I will send a test case. In the meantime, @corneliusroemer please use a subtree size <= 3741, sorry about that.

corneliusroemer commented 1 year ago

Oh noes! So that's one of those memory faults I'm not getting because of Rust 🙃

AngieHinrichs commented 1 year ago

Thanks to @yceh for the quick fix! You can peg it to 5000 again @corneliusroemer. 😄