ts_particles_export crash with Relion .star file

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Karine Mazmanian

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May 14, 2026, 6:12:56 AM (yesterday) May 14

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hi all,

I am running particle extraction with WarpTools ts_export_particles after Relion5 3D refinement, and it keeps crashing on me. I used run_data.star from relion 5 refine3d to re-extract my particles at a different pixel size with ts_export_particles. it worked before but stopped working after our admin updated warptools (my current version is 2.0.0dev39).

In the terminal i get a c# duplicate-key error, but if i check the worker log for the same tilt series, no error is reported and the particles look like they were successfully exported. (see the error messages below). I did some troubleshooting with Claude and Deepwiki, and workaround that worked for me was removing 10 columns from data_particles (rlnTomoParticleId, rlnTomoParticleName, rlnImageName, rlnTomoVisibleFrames, rlnGroupNumber, rlnClassNumber, rlnNormCorrection, rlnLogLikeliContribution, rlnMaxValueProbDistribution, rlnNrOfSignificantSamples). I want to check if anybody had met this error before and if I am doing something wrong.

command: WarpTools ts_export_particles \ --settings warp_tiltseries.settings \ --input_star relion_5.72Apx/Refine3D/job023/run_data.star \ --output_star relion_2.9Apx/extracted_proteasome_2.9Apx_224.star \ --coords_angpix 5.72 \ --output_angpix 2.86 \ --box 224 \ --diameter 450 \ --relative_output_paths \ --2d terminal

error: Failed to process /data/.../warp_tiltseries/Position_8.tomostar, marked as unselected
System.ArgumentException: An item with the same key has already been added. Key: rlnTomoParticleId at System.Collections.Generic.Dictionary`2.Add(TKey key, TValue value) at Warp.Star.AddColumn(String name, String[] values) in .../WarpLib/Star.cs:line 591 at WarpTools.Commands.ExportParticlesTiltseries.<>c__DisplayClass0_0.<Run>b__1(WorkerWrapper worker, TiltSeries tiltSeries) in .../WarpTools/Commands/Tiltseries/ExportParticlesTiltseries.cs:line 341

worker log for the same tilt series, no error: 2026-05-14 03:21:39.837 Received "TomoExportParticleSeries", with 6 arguments, for GPU #2, 11022 MB free: 2026-05-14 03:22:08.243 Exported 486 particles for /data/.../warp_tiltseries/Position_8.tomostar 2026-05-14 03:22:08.243 Execution took 28.405 seconds