I downloaded an OpenStreetMap extract for Europe, to a file latest.osm.pbf:

curl https://ftp5.gwdg.de/pub/misc/openstreetmap/download.geofabrik.de/europe-latest.osm.pbf \
-o latest.osm.pbf

I would like to extract all the waterways into a GPKG file. First, I perform the extraction using osmium tags-filter to a file waterways.osm.pbf:

osmium tags-filter -o waterways.osm.pbf latest.osm.pbf waterway

Then, I attempt to perform the .osm.pbf -> .gpkg conversion using ogr2ogr:

ogr2ogr waterway_lines.gpkg waterways.osm.pbf lines

This line produces a file, but the output indicates that something went wrong:

0...10...20...30...40...50...60...70..ERROR 1: failed to prepare SQL: INSERT INTO my_rtree VALUES (?,?,?,?,?)
.80...90...100 - done.

The produced waterway_lines.gpkg does show up in QGIS at low zoom levels:

enter image description here

But it disappears if I zoom in even slightly more.

ogr2ogr --version returns GDAL 3.8.5, released 2024/04/02

How do I fix failed to prepare SQL: INSERT INTO my_rtree VALUES (?,?,?,?,?) error when using ogr2ogr?

  • 2
    It seems something goes wrong while creating the spatial index. In a GDAL test I encounter something like that for MacOS ARM64, do you happen to work on that platform? A workaround is probably to drop and recreate the spatial index.
    – Pieter
    Apr 14 at 14:03
  • Yes, I am on MacOS ARM64 :| Thanks for the info!
    – zabop
    Apr 14 at 16:19

1 Answer 1


The error is related to this improvement that makes the creation of the spatial index much faster https://github.com/OSGeo/gdal/pull/8596. The idea behind that commit is to create the rtree tables with a custom method into another SQLite in-memory database, and as a final step copy the contents of the temporary tables into the main GeoPackage database. Something seems to fail in this process.

String "my_rtree" appears in a few places in the source code file https://github.com/OSGeo/gdal/blob/95579fe331493a2357062110d97e72be62b5c626/ogr/ogrsf_frmts/gpkg/ogrgeopackagetablelayer.cpp

The error comes probably after row #2933.

A workaround that should work is to create the GeoPackage table without spatial index by using layer creation option -LCO SPATIAL_INDEX=NO. Adding spatial index afterwards with ogrinfo should select another code path that does not use an in-memory database:

ogrinfo -sql "select CreateSpatialIndex(table_name,column_name)" my_gpkg

Consider sending mail to the gdal-dev mailing list and ask what might go wrong. Your dataset is rather large. I see that there is this comment in the source code:

"Too large in-memory RTree. "
"Flushing it and using memory friendly "
"algorithm for the rest"

Maybe the switch into another algorithm does not go fluently and triggers the error. You can test this hypothesis by making a test with a smaller OSM data extract.

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