Jonathon LeFaive

I have built a new package [minimac4-4.1.2-Linux-x86_64.sh.gz](https://github.com/statgen/Minimac4/files/10734853/minimac4-4.1.2-Linux-x86_64.sh.gz) and have tested it on rhel7, ubuntu18, and ubuntu20. Hopefully this will resolve both of your issues. Please let me know. Note: I...

The fallthrough is likely intentional swtich logic. The two lines that stand out to me in that log file are: ``` make[2]: Warning: File 'CMakeFiles/minimac4.dir/depend.make' has modification time 4.1 s...

The clock issue may be due to your build directory being on NFS. Maybe try building on a local disk (`/tmp` maybe).

> What change did you end up making? I changed the packaging image from Ubuntu to Alpine (https://github.com/statgen/Minimac4/commit/81fab63f10d2e9ea189bd7b2e162f1aee09f59a5).

I was able to reproduce this on centos7 this morning. I'm debugging now.

This appears to be an issue that only occurs on rhel7/centos7 (using both devtoolset-7 and devtoolset-8). I cannot reproduce this on centos8, rhel8, ubuntu16, or ubuntu18 using the default compilers....

> I noticed that the output imputed file dropped about 40% of the input SNPs. Should it be doing that? Probably not, unless you have an array with a lot...

Actually, neither Minimac4 nor the current version of savvy use htslib. Savvy is now a header-only library and the `src/savvy/*.cpp` files are dead code. I wonder whether using the default...

That wiki is legacy documentation. Use the readme in this repo instead. You can use the https protocol instead of ftp to download reference panel: https://share.sph.umich.edu/minimac4/panels/. You must index your...

I think you are using an old version of minimac4. See the latest at https://github.com/statgen/Minimac4/releases.