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The Zonal Statistics tool from the ArcGIS Spatial Analyst extension calculates statistics for zones defined by a zone dataset based on values from a value raster. In some instances, running the tool in ArcMap fails to generate an output raster and returns a generic error, "Error 999999: Error executing function."
Two possible reasons for this problem are:
• The requirements of the Esri Grid format, set as the format of the output raster, are not met. The Esri Grid format has specific requirements related to the file name, file location, path name, usage of special characters, and so forth. When the output raster format is not specified when running the tool, the default file format, Esri Grid, is automatically selected.
• The feature zone data contains more than 170,000 features.
Specify the output raster format as a TIFF file.
Ensure the requirements for the Esri Grid format are met. For more information about the Esri Grid format and the storage limitations associated with the format, refer to the following ArcGIS Help document, Esri Grid format.
Install ArcGIS for Desktop 10.2.1, 10.2.2, or 10.3. The 999999 error caused by a large number of input features is a known limitation in ArcGIS for Desktop versions 10.2 and earlier. This limitation has been resolved from versions 10.2.1 through 10.3.