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When you create an Inventory Resource Data Sync, it create a Glue database and the Amazon Athena queries are run against this database tables.
(-) https://docs.aws.amazon.com/systems-manager/latest/userguide/systems-manager-inventory-query.html
The "Table descriptor contains duplicate column" error indicates that there is a duplicate column name in Glue table schema.
(-) https://repost.aws/knowledge-center/athena-hive-invalid-metadata-duplicate
In order to fix the issue,
- Navigate to AWS Glue console --> Databases where you will find database with a name similar to the Resource Data Sync name
- Inside the database, find the table which is giving the error while querying through Athena (For Eg : AWS:InstanceInformation - Look at the "Location" column in the database)
- Click "Edit Schema" for the particular table and review the column names. You will find any one column being repeated twice.
- Delete one duplicate column
- Re-run the Athena query