The Zonal Statistics as Table tool from the Spatial Analyst toolbar creates statistical summaries for a raster within the zones of a value raster and reports the results to a table. Running the tool may fail with a generic error:
"Error 999999: Error executing function."
In some instances, along with the error message, the tool and ArcMap stop responding.
There are several possible reasons for this issue.
• The Zone field used to run the tool contains Null values.
• The Zone field name is greater than 17 characters in length.
• A large number of unique values are present in the raster dataset.
• The feature zone data used contains more than 170,000 features.
The 999999 error caused by a large number of input features is a known limitation in ArcGIS for Desktop 10.2 and earlier versions. This has been resolved in version 10.2.1 and later.