MarkovModel Error

[Benyapa-ins]

Hi,
I encountered only this error on chromosome 11; the rest is fine. I used this Docker image: biocontainers/minimac4:v1.0.0-2-deb_cv1.

minimac4: /build/minimac4-4XH9Mo/minimac4-1.0.0/src/MarkovModel.cpp:1072: void MarkovModel::foldProbabilities(std::vector&, int, ReducedHaplotypeInfo&, int, int): Assertion `foldProb[(*TempuniqueIndexMap)[i]]>0.0f' failed.

Could you please help me solve it? Thank you for your help!

Minimac4_chr11_log.txt

[jonathonl]

That image contains a very old version of Minimac4 that had some issues that allowed the HMM to get into a bad state. Also the image is using a debug build, which will be much slower than a release build. You should use the latest version found at https://github.com/statgen/Minimac4/releases/tag/v4.1.6. The newer versions require an update to the reference panel format (https://github.com/statgen/Minimac4?tab=readme-ov-file#reference-panel-creation).