The RUN directory is the primary output directory necessary for running Arachne. It is given as a subdirectory of DATA, and it has its own subdirectories, aptly named the SUBDIRs. Each RUN directory corresponds to a particular assembly in a genome project.
The RUN directory is where the binary output from pre-processing is stored. Assembly modules will use the files in RUN and write their output in SUBDIRs. Some modules, such as FinishNewReport, also write output files to RUN with generalized info about the assembly.
For example, the script Assemblez requires the following command-line form:
Assemblez PRE=/pre DATA=data RUN=run
If this succeeds, it will create
/pre/data/run/work, and put output there. Note that RUN must be a relative directory location, not be an absolute one (i.e., it cannot begin with a backslash.) However, RUN may contain internal backslashes, so that
/PRE/DATA/RUN is multiple steps below
/PRE/DATA in the directory tree.
Also note that the identity of RUN is different from Assemblez than it is for subsequent modules. If given RUN=run, Assemblez will create the subdirectory run and put assemblez.log and other useful files there. It will also create run/work and put all pre-processing output there, as well as all SUBDIRs. Any further modules you call must then specify RUN=run/work.