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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Typo: 'EROR' for 'ERROR' #118

Closed JocelynSP closed 4 years ago

JocelynSP commented 4 years ago

Describe the bug Error message encountered that is labelled \<EROR> , which makes it far too easy to miss in output Sample output: [2020-04-18 15:36:06] \<EROR> Encountered an exception during calling 'HaplotypeTree::prune_unique [2020-04-18 15:36:06] \<EROR> called with matching Haplotype not in tree'. This means there is a [2020-04-18 15:36:06] \<EROR> bug and your results are untrustworthy. [2020-04-18 15:36:06] \<EROR> [2020-04-18 15:36:06] \<EROR> To help resolve this error run in debug mode and send the log file to [2020-04-18 15:36:06] \<EROR> https://github.com/luntergroup/octopus/issues.

Version v1.4 sha256 = "14p61xk7jankp6gc26xciag9fnvm7r9vcbhclcy23f4ghf4q4sj1";

Additional context running from nixos / bionix

dancooke commented 4 years ago

This isn't a typo. All of the logging line labels are 4 characters long (e.g. INFO and WARN) to keep formatting consistent. Any EROR logging lines should appear at the end of the program since an error should always result in program termination, so they shouldn't be difficult to find.

JocelynSP commented 4 years ago

There is a considered decision (and I failed to follow up) - that's fair. We are running octopus as part of a complex pipeline, so when a build fails it is not immediately obvious which part failed, and the octopus program termination is not the final thing in the output.