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The really good news is that this task will be much easier with the OpenStudio Command Line Interface (CLI) coming out soon.

However, for your current script I think you may be calling the wrong version of the create method. I think you want to call this version of the create method:

  /// Creates a Job tree from the current workflow
  ///
  /// \param[in] outdir Output directory to be applied to the first job in the Workflow (child jobs inherit the outdir)
  /// \param[in] infile Input file to be attached to the first job in the workflow
  /// \param[in] epwdirorfile EPW file or directory containing EPW files to be search when looking for the appropriate
  ///                         EPW for energyplus simulation of infile
  /// \param[in] t_url_search_paths paths to search while normalizing any URLs in IDFs or OSMs that exist in the workflow
  openstudio::runmanager::Job create(
      const openstudio::path &outdir,
      const openstudio::path &infile,
      const openstudio::path &epwdirorfile = openstudio::path(),
      const std::vector<openstudio::URLSearchPath> &t_url_search_paths = std::vector<openstudio::URLSearchPath>());