Make the console output shorter and more informative

The console output of the workflow is very verbose but also includes [useful error messages](https://github.com/nextstrain/tb/blob/main/Snakefile#L139) that are not part of stderr. We should make the console output shorter and more informative [as discussed here](https://github.com/nextstrain/tb/pull/32#issuecomment-3465398308).