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When using the Query Builder in the Make Query Table tool to build an SQL query with two or more tables or feature classes (or both) as the input data, the tool fails to execute and returns the generic error 999999, with the following explanation:
Error: "ERROR 999999: Error executing function An expected Field was not found or could not be retrieved properly."
Note: This issue occurs in ArcGIS for Desktop 10.2.1, 10.2.2, 10.3, and 10.3.1. The bug ID logged for this issue is NIM-102585.
The error occurs because double quotes are added automatically to the SQL query expression in the Query Builder of the Make Query Table tool when there are two or more input data tables. String values with double quotes are considered invalid syntax in SQL query expressions.
Manually remove the double quotes from the SQL query expression for the tool to execute successfully.