I checked in with the MetaPhlAn developers about this and they informed me that MetaPhlAn has an --offline flag that will prevent this behavior when running in a grid context (for example). Adding that to your --metaphlan-options should solve this problem when MetaPhlAn is called inside of HUMAnN. We’ll likely make this a default in a future HUMAnN release to avoid users needing to know about it ahead of time.