General

General TreeSAPP functionality and behaviour

Checkpointing

TreeSAPP's checkpointing is controlled by the --stage parameter in most subcommands. It can be used for setting the final stage or setting the first stage to run from, depending on whether this is a fresh run or not.

• Example 1: treesapp assign output being written to a new directory (i.e. fresh run) with --stage place. In this scenario all stages up to and including phylogenetic placement (orf-call, search, align and place) will be executed but classify will not be completed.
• Example 2: Rerunning treesapp assign with a pre-existing output directory and --stage search. Here, TreeSAPP would first identify whether the 'intermediates/orf-call' directory was populated and proceed from the homology search stage until the end of the workflow. The ORF predictions from the previous run would be used.