As Liz suggested, the program isn’t able to open the SPECIATE VP output file for writing. Your RUNCTL file explicitly sets the locations for the GSPRO and GSCNV files, e.g.
The location of the SPECIATE VP output file isn’t configurable, and it tries to be written to a directory relative to the Speciation Tool’s “src” directory (…/outputs). This directory already exists as part of the Speciation Tool download package, so I’m not sure why the program can’t write to it. Maybe double-check the permissions, or if you’ve manually moved things around, make sure the outputs directory exists where expected.
Regarding the SPECIATE VP output file, I’m not sure what it’s used for (if anything). It’s not an input file needed for running SMOKE. There’s a sample output file provided in the outputs directory (outputs/SPECIATE5_VP.IVOCP6-SVOCN1.2020Mar18.txt). So it’s probably safe to ignore the error.