I have had similar issues. I go to the workbench / applilcation setting / resource locks
There you can release any locks that are present and then rerun your baseline. Here are a couple of helpful commands:
./runcommand.sh --help (Shows all the options)
Check if the user you are using to run script have read/write permission to all directories.
Also you can use below command to remove the lock
*eaccmd remove-all-flags --app <app_id>*
And make sure you are not doing any changes in workbench while running baseline, as it will lock the session for workbench user.