Keeping all humann2 temp files

Hi, I want to be able to see which files go into Minpath, and its configurations, but the logs reference temp files that don’t exist.

Is there an option for HUMAnN2 to keep all generated files?

HUMAnN2 creates two kinds of temp files during a run: 1) those we expect that the user might want to inspect (e.g. MetaPhlAn2 output) and 2) those that we do not expect the user to inspect (e.g. the working alignment files DIAMOND creates before reorganizing those data into tabular outputs).

Files of type 1 are kept by default but can be auto-deleted with the --remove-temp-output flag. Files of type 2 are never kept. The files you refer to belong to type 2 and there is no way to configure HUMAnN2 from the command-line to keep them. We consider such files to be working data structures that happen to be stored on disk during a run (e.g. due to their size or the constraints of external programs).