issue with Xenium Ranger 4.0

[BioinfoTongLI]

Thanks for the great tool!
I wonder if the latest version had been tested with xenium ranger 4.0?
I've seen this error with sereval versions of xenium analysis software version (1.4 4.0.1.0)

'test/XENIUM_RANGER_CS/XR_IMPORT_SEGMENTATION/XR_FINALIZE_IMPORT_SEGMENTATION/fork0/join-u004067faa8/files/cell_id_map.csv.gz' -> 'test/XENIUM_RANGER_CS/XR_SELECT_CELL_ID_MAP/fork0/chnk0-u004067faaf/files/cell_id_map.csv.gz'

And it worked fine with earlier xenium ranger. e.g. 3.1.1

[dcjones]

Did xenium ranger output anything else, or just this?

[BioinfoTongLI]

Thanks for your prompt reply!
there are a bunch other things as well:

2026-01-14 21:25:49 [runtime] (join_complete)   ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_IMPORT_SEGMENTATION.XR_FINALIZE_IMPORT_SEGMENTATION
  2026-01-14 21:27:16 [runtime] (chunks_complete) ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_RELABEL.XR_SUBSAMPLE_TRANSCRIPTS
  2026-01-14 21:27:16 [runtime] (run:local)       ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_RELABEL.XR_SUBSAMPLE_TRANSCRIPTS.fork0.join
  2026-01-14 21:33:17 [runtime] (update)          ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_RELABEL.XR_SUBSAMPLE_TRANSCRIPTS.fork0 join_running
  2026-01-14 21:34:41 [runtime] (join_complete)   ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_RELABEL.XR_SUBSAMPLE_TRANSCRIPTS
  2026-01-14 21:36:20 [runtime] (ready)           ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_RELABEL.XR_FINALIZE_RELABEL
  2026-01-14 21:36:20 [runtime] (run:local)       ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_RELABEL.XR_FINALIZE_RELABEL.fork0.chnk0.main
  2026-01-14 21:37:47 [runtime] (chunks_complete) ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_RELABEL.XR_FINALIZE_RELABEL
  2026-01-14 21:38:31 [runtime] (ready)           ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_IMPORT_TRANSCRIPT_ASSIGNMENTS
  2026-01-14 21:38:31 [runtime] (ready)           ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.INSITU_COUNTER_CS.INSITU_COUNTER_CORE.XR_UNZIP_TRANSCRIPTS
  2026-01-14 21:38:31 [runtime] (run:local)       ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.INSITU_COUNTER_CS.INSITU_COUNTER_CORE.XR_UNZIP_TRANSCRIPTS.fork0.chnk0.main
  2026-01-14 21:38:31 [runtime] (ready)           ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.MERGE_METRICS
  2026-01-14 21:38:31 [runtime] (run:local)       ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.MERGE_METRICS.fork0.chnk0.main
  2026-01-14 21:38:31 [runtime] (ready)           ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.SELECT_CELLS_DATASET
  2026-01-14 21:38:31 [runtime] (run:local)       ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.SELECT_CELLS_DATASET.fork0.chnk0.main
  2026-01-14 21:38:31 [runtime] (ready)           ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_SELECT_CELL_ID_MAP
  2026-01-14 21:38:31 [runtime] (run:local)       ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_SELECT_CELL_ID_MAP.fork0.chnk0.main
  2026-01-14 21:38:32 [runtime] (failed)          ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_SELECT_CELL_ID_MAP
  2026-01-14 21:38:32 [runtime] (chunks_complete) ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.SELECT_CELLS_DATASET
  
  [error] Pipestance failed. Error log at:
  OS_AQsb3-TUM-0-FO-1-S13-A1/XENIUM_RANGER_CS/XR_SELECT_CELL_ID_MAP/fork0/chnk0-u003d680cd7/_errors
  
  Log message:
  Traceback (most recent call last):
    File "/xeniumranger-xenium4.0/external/martian/adapters/python/martian_shell.py", line 648, in _main
      stage.main()
    File "/xeniumranger-xenium4.0/external/martian/adapters/python/martian_shell.py", line 607, in main
      self._run(lambda: self._module.main(args, outs))
    File "/xeniumranger-xenium4.0/external/martian/adapters/python/martian_shell.py", line 564, in _run
      cmd()
    File "/xeniumranger-xenium4.0/external/martian/adapters/python/martian_shell.py", line 607, in <lambda>
      self._run(lambda: self._module.main(args, outs))
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/xeniumranger-xenium4.0/mro/insitu/stages/xr_select_cell_id_map/__init__.py", line 40, in main
      hardlink_file_with_fallback(selected, outs.cell_id_map)
    File "/xeniumranger-xenium4.0/lib/python/turing/engine/infra/utils/file_utils.py", line 237, in hardlink_file_with_fallback
      os.link(src, dst)
  FileNotFoundError: [Errno 2] No such file or directory: 'OS_AQsb3-TUM-0-FO-1-S13-A1/XENIUM_RANGER_CS/XR_IMPORT_SEGMENTATION/XR_FINALIZE_IMPORT_SEGMENTATION/fork0/join-u003d6809bc/files/cell_id_map.csv.gz' -> 'OS_AQsb3-TUM-0-FO-1-S13-A1/XENIUM_RANGER_CS/XR_SELECT_CELL_ID_MAP/fork0/chnk0-u003d680cd7/files/cell_id_map.csv.gz'

[dcjones]

I haven't been able to reproduce this issue, I was able to run a xenium dataset through proseg and xenium ranger 4.0.1.1. Are you using the latest version of proseg (3.1.0)?

Unfortunately this output isn't too revealing. It references an error log though, so maybe you can paste the contents of OS_AQsb3-TUM-0-FO-1-S13-A1/XENIUM_RANGER_CS/XR_SELECT_CELL_ID_MAP/fork0/chnk0-u003d680cd7/_errors.

[BioinfoTongLI]

Hi @dcjones , yes I can confirm that it's xenium ranger 4.0.1.1 and proseg 3.1.0.
and unfortunately, in the file OS_AQsb3-TUM-0-FO-1-S13-A1/XENIUM_RANGER_CS/XR_SELECT_CELL_ID_MAP/fork0/chnk0-u003d680cd7/_errors. it's exactly the same error message that I've sent above.
I will test with more datasets and see if there's any other variable that might be useful.
Will keep you updated here

[dcjones]

Ok, I'll try on some other datasets as well and see if I can reproduce the issue. As a last resort, you could also find a way to share either the original dataset or the proseg output with me and I could try to reproduce the issue that way.