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HyPhy: Hypothesis testing using Phylogenies
http://www.hyphy.org
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GARD: Internal error in ComputeBranchCache #1688

Closed matthewglasenapp closed 7 months ago

matthewglasenapp commented 7 months ago

I receive the following error when running gard on a large multiple sequence alignment (9 sequences of 7575 bases each). The error was seemingly produced during the 12 breakpoint analysis. Gard has worked fine for me on smaller sequence alignments. Any tips would be greatly appreciated.

hyphy gard --alignment sequence_alignment.phylip

Error: Internal error Internal error in ComputeBranchCache (branch gard.tree.part_4.Node9, eval #553580214 ) reversible model cached likeli hood = -67.49786829839633, directly computed likelihood = -79.91359631404707. This is most likely because a non-r eversible model was incorrectly auto-detected (or specified by the model file in environment variables; for smaller e rrors, this could be due to numerical instability of calculations for larger alignments).

errors.log.txt gard_output.txt sequence_alignment.phylip.best-gard.fit.bf.txt sequence_alignment.phylip.best-gard.txt sequence_alignment.phylip.GARD.json sequence_alignment.phylip.txt

stevenweaver commented 7 months ago

Dear @matthewglasenapp,

Would you mind reviewing https://github.com/veg/hyphy/issues/1610 and seeing if this matches the issue you are having?

If you have a recent enough version of hyphy, you should be able to use the ENV="TOLERATE_NUMERICAL_ERRORS=1;" command line argument to avoid this error.

Best, Steven

matthewglasenapp commented 7 months ago

Thanks so much, Steven. That option worked with version 2.5.50.

hyphy ENV="TOLERATE_NUMERICAL_ERRORS=1;" gard --alignment sequence_alignment.phylip