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In QGIS 2.16.2 I am trying to intersect two Shapefiles to create a third Shapefile, however the Intersection tool is only allowing Save file as DBR, CSV, XLSX or ODS - not SHP. One of the Shapefiles was just made and saved using Intersection Run as Batch Process in this project.

If I start a new project and add the Shapefiles I can intersect and create a third Shapefile. I've intersected Shapefiles created from intersected Shapefiles in the same project before and not had this problem.

File1.shp intersect w/ IntersectedFile2.shp should make IntersectedFile3.shp - Does not work in the same project where IntersectedFile2.shp was created. Works in new project.

Is this a bug or am I missing something?

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    Sounds like there's no geometry in the result, and QGIS can only save it as a table. Do the two things you are intersecting actually overlap at all? Can you give us the data or examples that do the same? – Spacedman Jan 7 '17 at 9:17
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    I just tried intersecting two non-overlapping layers and could save a shapefile with 0 features, which seems to be the right thing. So that doesn't explain your problem, sorry. Think we need your data... – Spacedman Jan 7 '17 at 9:23
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    could be that you have a mixed geometry output which also can't be saved to a single shapefile – Ian Turton Jan 7 '17 at 11:42
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I had the same problem.

I tried using the v.clean tool, then resaved and it worked.

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