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I'm trying to extract bathymetry of Mediterranean Sea raster GeoTIFF file (downloaded from https://www.bodc.ac.uk/data/hosted_data_systems/gebco_gridded_bathymetry_data/gebco_30_second_grid/) from bathymetry (vector mask layer) downloaded from Natural Earth data.

After I selected bathymetry depth 0 at query builder of the vector layer, used Raster > Extraction > Clip raster by mask layer, but the area of elevation its grayed and not deleted.

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I tried save as both layers raster and vector with same CRS WGS 84 and still the same result. After save as the raster GeoTIFF (GEBCO2014_-12.3),(Gebco 4326 GeoTIFF) in CRS WGS 84 used again Raster > Extraction > Clip raster by mask layer. enter image description here

How can i resolve this ?

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    Ensure that your raster data and your vector data share the same coordinate reference system before executing the clip. Some tools fail when this is not the case. – GBG Jan 26 at 0:23
  • Please Edit the question to add details requested in comments. It's not fair to those who would help to force them to need to sift through comments for critical information. – Vince Jan 26 at 14:45
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With the QGIS GDAL process it is impossible to clip the raster INT16 GeoTIFF downloaded from GEBCO_2014 Grid (30 arc-second interval) so i downloaded the SCP plugin and used Band set > Preprocessing > Clip multiple rasters. The result was fine the raster was clipped well by the polygon layer bathymetry level 0 but had some issues at value 1000 (missing pixels at depth 1000)

enter image description here.

So i thought that the problem could be at INT16 GeoTIFF file type and downloaded from GEBCO_2014 Grid (30 arc-second interval) ESRI ASCII and Save as GeoTIFF with the same projection of bathymetry polygon layer. After reopen the raster GeoTIFF used Raster > Extraction > Clip raster by mask layer and was clipped as i wanted without any issues.

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