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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
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Longshot `thread 'main' panicked at 'assertion failed: p <= 0.0'` error: possible to update longshot? #109

Closed KatSteinke closed 2 years ago

KatSteinke commented 2 years ago

Would it be possible to use a newer version of longshot? Since January I've been intermittently getting thread 'main' panicked at 'assertion failed: p <= 0.0' errors when using longshot, which should be fixed in longshot 0.4.3 and up (see the relevant issue there). However, ARTIC has longshot 0.4.1 pinned as a dependency. With longshot 0.4.5 now available on conda, would it be possible for ARTIC to use a higher version at some point to avoid this issue?

BioWilko commented 2 years ago

I'll test a version >=0.4.3 to ensure full compatibility but assuming all is well I will update the pinned version with the next conda release, however if you wish to try this locally you can do so by installing from source and updating the version in environment.yml prior to solving the conda environment.

KatSteinke commented 2 years ago

I've finally gotten around to trying this for myself locally. Have been trying it with something that reliably fails using longshot 0.4.1 and it works with longshot 0.4.5, and the update doesn't break my usual test dataset either, so I'll go ahead and create a pull request.

BioWilko commented 2 years ago

Version 1.2.3 now pins a version of longshot >= 0.4.5 to fix this and a few other errors.