Proseg/3.0.2 to xeniumranger import-segmentation error

[bk11-lab]

Hi, I ran the following commands for my Xenium output. However, the command #3 failed with the following error. What could be the problem and how can it be fixed?

command #1
proseg --xenium transcripts.parquet

command #2
proseg-to-baysor proseg-output.zarr --output-transcript-metadata proseg-to-baysor-transcript-metadata.csv --output-cell-polygons proseg-to-baysor-cell-polygons.geojson

command #3
xeniumranger import-segmentation \
	--id tma2_proseg \
	--xenium-bundle /User/scratch/TMA-2__20250723__163520/ \
	--transcript-assignment proseg-to-baysor-transcript-metadata.csv \
	--viz-polygons proseg-to-baysor-cell-polygons.geojson \
	--units=microns

I got the following error:

2025-08-15 23:12:15 [runtime] Found orphaned stage: ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.INSITU_COUNTER_CS.METRIC_CALCULATOR_CS.GENERATE_SAMPLE_METRICS
2025-08-15 23:12:15 [runtime] (reset-partial)   ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.INSITU_COUNTER_CS.INSITU_COUNTER_CORE.INSITU_ANALYZER.RUN_PCA.fork0.chnk0
2025-08-15 23:12:26 [runtime] (split_complete)  ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.INSITU_COUNTER_CS.INSITU_COUNTER_CORE.INSITU_ANALYZER.RUN_PCA
2025-08-15 23:12:26 [runtime] (run:local)       ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.INSITU_COUNTER_CS.INSITU_COUNTER_CORE.INSITU_ANALYZER.RUN_PCA.fork0.chnk0.main
2025-08-15 23:12:26 [runtime] (split_complete)  ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.INSITU_COUNTER_CS.METRIC_CALCULATOR_CS.GENERATE_SAMPLE_METRICS
2025-08-15 23:12:26 [runtime] (run:local)       ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.INSITU_COUNTER_CS.METRIC_CALCULATOR_CS.GENERATE_SAMPLE_METRICS.fork0.join
2025-08-15 23:12:40 [runtime] (failed)          ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.INSITU_COUNTER_CS.INSITU_COUNTER_CORE.INSITU_ANALYZER.RUN_PCA

[error] Pipestance failed. Error log at:
tma2_proseg/XENIUM_RANGER_CS/INSITU_COUNTER_CS/INSITU_COUNTER_CORE/INSITU_ANALYZER/RUN_PCA/fork0/chnk0-u1d2b9fbecf/_errors

Log message:
Job failed in stage code

signal: illegal instruction (core dumped)


Waiting 6 seconds for UI to do final refresh.
Pipestance failed. Use --noexit option to keep UI running after failure.

2025-08-15 23:12:46 Shutting down.
Could not get disk stats for /opt/weka/data/agent/tmpfss/cgroup/weka: permission denied
Saving pipestance info to "tma2_proseg.mri.tgz"
tar: Removing leading `/' from member names
tar: Removing leading `/' from hard link targets
For assistance, upload this file to 10x Genomics by running:

xeniumranger upload <your_email> "tma2_proseg.mri.tgz"

[dcjones]

Could you post the contents of the error log it references (tma2_proseg/XENIUM_RANGER_CS/INSITU_COUNTER_CS/INSITU_COUNTER_CORE/INSITU_ANALYZER/RUN_PCA/fork0/chnk0-u1d2b9fbecf/_errors)?

[bk11-lab]

Thank you for the reply. Please see the following for content of _errors.

cat tma2_proseg/XENIUM_RANGER_CS/INSITU_COUNTER_CS/INSITU_COUNTER_CORE/INSITU_ANALYZER/RUN_PCA/fork0/chnk0-ube159fdfe5/_errors
Job failed in stage code

signal: illegal instruction (core dumped)

[dcjones]

Well, that was less useful than I had hoped! You may have to contact 10x support since this doesn't give me much to go on, and they would be better positioned to figure out what went wrong. If they discover something wrong with the input, I'm happy to fix it.