I am working on a large shapefile sourced from https://www.iucnredlist.org/resources/spatial-data-download. I cannot clip Fish and Plants (global file) in Freshwater groups species to a smaller extent (country level).

I tried clipping in QGIS but could not get the output. QGIS return an error: intersection failed. However, the clip works perfectly fine for all other datasets. I have successfully clipped other (smaller in size) shapefiles. I found a link where it suggested using 'Clip by extent' in GDAL, but it gave an empty shapefile having no data.

How can it be solved?

enter image description here

For the extent, let's say, I want to clip it to India's extent. In QGIS, the error is:

enter image description here

  • I checked the shared URL and I suspect it's the first one on the List? Add a few screenshots of the extent you are working with and the returned error message when trying to clip in QGIS, as ArcMap crashes. May 18, 2022 at 6:32
  • If you also want to ask about ArcMap then please do that in a separate question.
    – PolyGeo
    May 18, 2022 at 7:19
  • @YogeshChavan I want to clip it to India's extent. In qgis, I am getting error: intersection failed. I have started process and attach screenshot when it finishes.
    – rgt
    May 18, 2022 at 8:50

1 Answer 1


In QGIS try:

  1. Fix geometries, save the output as geopackage.
  2. Create spatial index.
  3. Clip

If it still doesnt work:

  1. Multipart to Singlepart the spatial index output.

  2. Create spatial index

  3. Clip

  • can you please elaborate your steps? or please provide some links for these steps. I am quite new to GIS analysis, not able to follow these.
    – rgt
    May 18, 2022 at 8:52
  • @rgt Also save shapefile as geopackage before processing. May 18, 2022 at 11:10
  • 1
    Fix Geometries worked. First I had to use fixed geometries, then the resulting file used for clipping produced desired result.
    – rgt
    Aug 3, 2022 at 12:10

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