I have a shapefile with 31 million polygons and I want to extract statistics from a raster for each polygon. Whenever I use zonal statistics I get:

ERROR 999998: Unexpected Error. Failed to execute (Zonal Statistics)

The problem with this error is that there is no clear answer on what is going wrong.

So far I tried breaking the shapefile into smaller pieces and run zonal statistics, changed the processing from background to foreground and changed my working directory to C:/ but I keep getting the same error.

I would like to know what else can I try?

  • 4
    Are your polygons overlapping? If not, have you tried manually converting your input polygons to raster? See the docs
    – Barbarossa
    Commented Mar 16, 2016 at 19:11
  • Thanks for your answer, there are no overlapping polygons. Now I'm converting my polygons to raster but it should take some time before I can test if it works.
    – john doe
    Commented Mar 16, 2016 at 19:34
  • 1
    From ESRI's help on zonal stats: "If the zone input is a feature dataset, a vector-to-raster conversion will be internally applied to it". You might as well do it yourself and be in total control of the settings. Plus, it will help you to isolate any unknown errors.
    – Tom
    Commented Mar 16, 2016 at 19:40
  • 1
    Be extremely careful with the cell size, it could be size of the raster causing problems. You might try this gis.stackexchange.com/questions/112946/… it works for overlapping polygons, should work in your case
    – FelixIP
    Commented Mar 17, 2016 at 1:06
  • Thank you very much guys that was it. I converted the polygons to raster manually, the size of the raster was a bit tricky but in the end it worked.
    – john doe
    Commented Mar 18, 2016 at 11:18

1 Answer 1


In ArcGIS you could try running Data Management Tools>Features>Check Geometry first (and Repair Geometry if needed). You could also try using Zonal Statistics in QGIS (it also has a repair geometry -kind-of-function).

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