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You can call APEX Data Loader APIs from commandline. So, you write your queries and set up a cronjob to schedule run apex data loader to get you whatever you need. The data export will be in the files (in your specified directories).
The only issue is what if it fails to run and something happens during the data loader execution. For that, you'd have to write a program for example in java and handle error appropriately. You'd do this if it's mission critical. Otherwise, my first suggestion above should be enough to cater your needs.