Error in `create_mobie_project`

[Buglakova]

I tried to rerun the pipeline from scratch and get the following error in create_mobie_project:

Traceback (most recent call last):
  File "/g/kreshuk/buglakova/projects/matchmaker/matchmaker/mobie_export.py", line 163, in <module>
    main()
  File "/home/buglakov/miniconda3/envs/matchmaker_env/lib/python3.11/site-packages/click/core.py", line 1462, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/buglakov/miniconda3/envs/matchmaker_env/lib/python3.11/site-packages/click/core.py", line 1383, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/buglakov/miniconda3/envs/matchmaker_env/lib/python3.11/site-packages/click/core.py", line 1246, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/buglakov/miniconda3/envs/matchmaker_env/lib/python3.11/site-packages/click/core.py", line 814, in invoke
    return callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/g/kreshuk/buglakova/projects/matchmaker/matchmaker/mobie_export.py", line 151, in main 
    export_to_mobie(
  File "/g/kreshuk/buglakova/projects/matchmaker/matchmaker/mobie_export.py", line 115, in export_to_mobie
    add_to_mobie(input_path, input_key, mobie_folder, dataset_name, segmentation_name, menu_name)
  File "/g/kreshuk/buglakova/projects/matchmaker/matchmaker/mobie_export.py", line 35, in add_to_mobie
    add_segmentation(
  File "/home/buglakov/miniconda3/envs/matchmaker_env/lib/python3.11/site-packages/mobie/segmentation.py", line 93, in add_segmentation
    import_segmentation(input_path, input_key, data_path,
  File "/home/buglakov/miniconda3/envs/matchmaker_env/lib/python3.11/site-packages/mobie/import_data/segmentation.py", line 42, in import_segmentation
    add_max_id(in_path, in_key, out_path, out_key, tmp_folder, target, max_jobs)
  File "/home/buglakov/miniconda3/envs/matchmaker_env/lib/python3.11/site-packages/mobie/import_data/utils.py", line 134, in add_max_id
    with open_file(out_path, "r") as f_out:
         ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/buglakov/miniconda3/envs/matchmaker_env/lib/python3.11/site-packages/elf/io/files.py", line 71, in open_file
    return constructor(path, mode=mode, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/buglakov/miniconda3/envs/matchmaker_env/lib/python3.11/site-packages/z5py/file.py", line 84, in __init__
    raise OSError(errno.EROFS, os.strerror(errno.EROFS), handle.path())
OSError: [Errno 30] Read-only file system: 'data/test_registration/mobie_project/platy1_muscles_stardist/images/ome-zarr/fixed_image_input.ome.zarr'

I checked and it looks like platy1_muscles_stardist/images/ doesn't exist yet, so it can't create a directory in it. @Marei33, do you have the same?

[Marei33]

Hi @Buglakova , on which branch are you working? I don't get the error, so it's hard to tell what might be the reason

[Buglakova]

It is the last commit of dev branch. I think it might be the problem only with a fresh run where there are no datasets in mobie project yet.

[Marei33]

But for me it works also when I delete the complete mobie project folder/ test registration folder...

[zh320]

also encounter an error when running snakemake using the latest dev branch @Marei33 .

Exiting because a job execution failed. Look below for error messages
[Fri Jan 16 15:18:30 2026]
Error in rule create_mobie_project:
    message: None
    jobid: 4
    input: data/test_registration/fixed_image.n5/input, data/test_registration/moving_image.n5/input, data/test_registration/fixed_image.n5, data/test_registration/moving_image.n5
    output: data/test_registration/mobie_project/platy1_muscles_stardist/images/ome-zarr/fixed_image_input.done, data/test_registration/mobie_project/platy1_muscles_stardist/images/ome-zarr/moving_image_input.done
    log: data/test_registration/matchmaker.log (check log file(s) for error details)
    shell:
        python matchmaker/mobie_export.py --input_path data/test_registration/fixed_image.n5 --input_key input --input_type fixed --dataset_name platy1_muscles_stardist --output_dir data/test_registration;touch data/test_registration/mobie_project/platy1_muscles_stardist/images/ome-zarr/fixed_image_input.done;rm -rf ./tmp_platy1_muscles_stardist_fixed_image_input;python matchmaker/mobie_export.py --input_path data/test_registration/moving_image.n5 --input_key input --input_type moving --dataset_name platy1_muscles_stardist --output_dir data/test_registration;touch data/test_registration/mobie_project/platy1_muscles_stardist/images/ome-zarr/moving_image_input.done;rm -rf ./tmp_platy1_muscles_stardist_moving_image_input;

[zh320]

Not sure what caused the problem, but I was able to resolve it by deleting the .mobie folder and reinstalling mobie_utils. I can now run the snakemake workflow without errors.

[Buglakova]

Interesting. What was in .mobie? Do you think it was because of some temporary files which were not deleted correctly earlier?

[zh320]

Interesting. What was in .mobie? Do you think it was because of some temporary files which were not deleted correctly earlier?

The .mobie folder contains *.schema.json files that are probably used to define the project structure. They are not temporary files. My previous runtime error might be due to these files containing invalid strings or formats.

[Buglakova]

Ok, let's keep an eye on this and see how to reproduce this error when it comes up again. Do you think deleting the directory was enough or it was really necessary to reinstall?

[constantinpape]

FYI: this error was due to the fact that the ome.ngff json-schema url was changed, which led to invalid strings in the corrsponding json schema file. It was fixed here: mobie/mobie-utils-python#142 .

[zh320]

Ok, let's keep an eye on this and see how to reproduce this error when it comes up again. Do you think deleting the directory was enough or it was really necessary to reinstall?

Probably deleting the .mobie folder is enough. This folder will be downloaded when running the workflow.