The SUBDIR directories are output subdirectories containing draft assemblies. Each SUBDIR corresponds to a step in the assembly process. SUBDIR is given as a subdirectory of RUN; note that SUBDIR must be a relative directory location, not be an absolute one (i.e., it cannot begin with a backslash.) The files in a SUBDIR include fasta, qual, and text files describing reads, contigs, and supercontigs.
Every time an assembly module is run, it takes input from an existing SUBDIR and/or from the RUN directory. It then either modifies the existing SUBDIR, usually by adding new files to it, or it creates a new SUBDIR (now called OUTDIR) and puts its output there. If a module expects the command-line argument OUTDIR, it will create OUTDIR accordingly. If it expects SUBDIR but not OUTDIR, you may assume that it edits the SUBDIR in place.