Detect missing environment variables sooner

[morungos]

I just ran a subtraction using GRA and when it got to the GRA stage, it crashed out with the error "Missing environment variable: READSCAN_PATHOGEN_REF". Yes, this is correct, but that should happen before any subtraction logic was applied, when we are using GRA, so that the database is consistent. Also, that avoids a half hour wait to get to that stage and fail.