Segger fails on compute environment

[rcannood]

On a gpu enabled node:

/etc/bash.bashrc: line 9: PS1: unbound variable

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "/scratch/3p2VK70UaoOHsN/c0/a5d4209de158d717c4507b3d14daa6/.viash_script.py", line 13, in <module>
    import torch
  File "/usr/local/lib/python3.12/dist-packages/torch/__init__.py", line 2248, in <module>
    from torch import quantization as quantization  # usort: skip
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/__init__.py", line 2, in <module>
    from .fake_quantize import *  # noqa: F403
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/fake_quantize.py", line 10, in <module>
    from torch.ao.quantization.fake_quantize import (
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/__init__.py", line 12, in <module>
    from .pt2e._numeric_debugger import (  # noqa: F401
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/_numeric_debugger.py", line 9, in <module>
    from torch.ao.quantization.pt2e.graph_utils import bfs_trace_with_node_process
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/graph_utils.py", line 9, in <module>
    from torch.export import ExportedProgram
  File "/usr/local/lib/python3.12/dist-packages/torch/export/__init__.py", line 60, in <module>
    from .decomp_utils import CustomDecompTable
  File "/usr/local/lib/python3.12/dist-packages/torch/export/decomp_utils.py", line 5, in <module>
    from torch._export.utils import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/__init__.py", line 48, in <module>
    from .wrappers import _wrap_submodules
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/wrappers.py", line 7, in <module>
    from torch._higher_order_ops.flat_apply import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/__init__.py", line 1, in <module>
    from torch._higher_order_ops._invoke_quant import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/_invoke_quant.py", line 8, in <module>
    from torch._higher_order_ops.base_hop import BaseHOP, FunctionWithNoFreeVars
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/base_hop.py", line 12, in <module>
    from torch._subclasses.functional_tensor import disable_functional_mode
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 46, in <module>
    class FunctionalTensor(torch.Tensor):
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 279, in FunctionalTensor
    cpu = _conversion_method_template(device=torch.device("cpu"))
/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py:279: UserWarning: Failed to initialize NumPy: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

 (Triggered internally at /opt/pytorch/pytorch/torch/csrc/utils/tensor_numpy.cpp:81.)
  cpu = _conversion_method_template(device=torch.device("cpu"))
Using device: cuda
Reading input: _viash_par/input_1/spatial_unlabelled.zarr
Input:  SpatialData object, with associated Zarr store: /scratch/3p2VK70UaoOHsN/stage-14b82b41-b3e7-4a30-9b6d-1b4df3c97782/c7/d378169abc01fdf607d59f34830514/spatial_unlabelled.zarr
├── Images
│     └── 'image': DataTree[cyx] (1, 1000, 1000), (1, 500, 500), (1, 250, 250), (1, 125, 125), (1, 62, 62)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (1000, 1000), (500, 500), (250, 250), (125, 125), (62, 62)
│     └── 'nucleus_labels': DataTree[yx] (1000, 1000), (500, 500), (250, 250), (125, 125), (62, 62)
├── Points
│     └── 'transcripts': DataFrame with shape: (<Delayed>, 8) (3D points)
└── Tables
      └── 'table': AnnData (0, 424)
with coordinate systems:
    ▸ 'global', with elements:
        image (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points)
Init segmentation mode: None
Traceback (most recent call last):
  File "/scratch/3p2VK70UaoOHsN/c0/a5d4209de158d717c4507b3d14daa6/.viash_script.py", line 339, in <module>
    raise ValueError(f"Unknown init_segmentation mode: {mode}")
ValueError: Unknown init_segmentation mode: None

task-10.command.out.txt
task-10.command.err.txt
task-10.command.log.txt

[rcannood]

After #46:

Traceback (most recent call last):
  File "/usr/local/bin/segger", line 6, in
    sys.exit(app())
             ^^^^^
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/core.py", line 1947, in __call__
    result = _run_maybe_async_command(command, bound, resolved_backend)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/_run.py", line 50, in _run_maybe_async_command
    return command(*bound.args, **bound.kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/segger/cli/segment.py", line 312, in segment
    from ..data import ISTDataModule
  File "/usr/local/lib/python3.12/dist-packages/segger/data/__init__.py", line 1, in
    from .data_module import ISTDataModule
  File "/usr/local/lib/python3.12/dist-packages/segger/data/data_module.py", line 20, in
    from ..io import (
  File "/usr/local/lib/python3.12/dist-packages/segger/io/__init__.py", line 1, in
    from .preprocessor import get_preprocessor
  File "/usr/local/lib/python3.12/dist-packages/segger/io/preprocessor.py", line 14, in
    from .cosmx import get_cosmx_polygons
  File "/usr/local/lib/python3.12/dist-packages/segger/io/cosmx.py", line 11, in
    from .utils import masks_to_contours, contours_to_polygons
  File "/usr/local/lib/python3.12/dist-packages/segger/io/utils.py", line 6, in
    import cv2
  File "/usr/local/lib/python3.12/dist-packages/cv2/__init__.py", line 181, in
    bootstrap()
  File "/usr/local/lib/python3.12/dist-packages/cv2/__init__.py", line 153, in bootstrap
    native_module = importlib.import_module("cv2")
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/importlib/__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: libxcb.so.1: cannot open shared object file: No such file or directory
Traceback (most recent call last):
  File "/scratch/5XVXMdmr4zRgCS/1a/1a253f984df4af27387127b77c80f5/.viash_script.py", line 384, in
    seg_pq = _run_segger(xenium_dir, segger_out_dir)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/scratch/5XVXMdmr4zRgCS/1a/1a253f984df4af27387127b77c80f5/.viash_script.py", line 268, in _run_segger
    subprocess.run(cmd, check=True, env=env)
  File "/usr/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['segger', 'segment', '-i', '/tmp/segger_274/xenium_input', '-o', '/tmp/segger_274/segger_output', '--n-epochs', '20', '--prediction-expansion-ratio', '0.5', '--prediction-mode', 'nucleus']' returned non-zero exit status 1.

[rcannood]

@EliHei2 With #49 :

/etc/bash.bashrc: line 9: PS1: unbound variable

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "/scratch/2vU8vpPrOaSTxY/46/343393a7896a8c3116d8804591dec8/.viash_script.py", line 12, in <module>
    import torch
  File "/usr/local/lib/python3.12/dist-packages/torch/__init__.py", line 2248, in <module>
    from torch import quantization as quantization  # usort: skip
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/__init__.py", line 2, in <module>
    from .fake_quantize import *  # noqa: F403
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/fake_quantize.py", line 10, in <module>
    from torch.ao.quantization.fake_quantize import (
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/__init__.py", line 12, in <module>
    from .pt2e._numeric_debugger import (  # noqa: F401
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/_numeric_debugger.py", line 9, in <module>
    from torch.ao.quantization.pt2e.graph_utils import bfs_trace_with_node_process
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/graph_utils.py", line 9, in <module>
    from torch.export import ExportedProgram
  File "/usr/local/lib/python3.12/dist-packages/torch/export/__init__.py", line 60, in <module>
    from .decomp_utils import CustomDecompTable
  File "/usr/local/lib/python3.12/dist-packages/torch/export/decomp_utils.py", line 5, in <module>
    from torch._export.utils import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/__init__.py", line 48, in <module>
    from .wrappers import _wrap_submodules
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/wrappers.py", line 7, in <module>
    from torch._higher_order_ops.flat_apply import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/__init__.py", line 1, in <module>
    from torch._higher_order_ops._invoke_quant import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/_invoke_quant.py", line 8, in <module>
    from torch._higher_order_ops.base_hop import BaseHOP, FunctionWithNoFreeVars
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/base_hop.py", line 12, in <module>
    from torch._subclasses.functional_tensor import disable_functional_mode
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 46, in <module>
    class FunctionalTensor(torch.Tensor):
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 279, in FunctionalTensor
    cpu = _conversion_method_template(device=torch.device("cpu"))
/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py:279: UserWarning: Failed to initialize NumPy: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

 (Triggered internally at /opt/pytorch/pytorch/torch/csrc/utils/tensor_numpy.cpp:81.)
  cpu = _conversion_method_template(device=torch.device("cpu"))
Using device: cuda
Reading input: _viash_par/input_1/spatial_unlabelled.zarr
Input:  SpatialData object, with associated Zarr store: /scratch/2vU8vpPrOaSTxY/stage-a2c410da-497f-47b5-8aab-48d0f8e8f691/7e/9157b87ca40a6721d21652ad081072/spatial_unlabelled.zarr
├── Images
│     └── 'image': DataTree[cyx] (1, 1000, 1000), (1, 500, 500), (1, 250, 250), (1, 125, 125), (1, 62, 62)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (1000, 1000), (500, 500), (250, 250), (125, 125), (62, 62)
│     └── 'nucleus_labels': DataTree[yx] (1000, 1000), (500, 500), (250, 250), (125, 125), (62, 62)
├── Points
│     └── 'transcripts': DataFrame with shape: (<Delayed>, 8) (3D points)
└── Tables
      └── 'table': AnnData (0, 424)
with coordinate systems:
    ▸ 'global', with elements:
        image (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points)
Init segmentation mode: transcript_cell_id
Initial segmentation: 307 polygons
Running segger: segger segment -i /tmp/segger_293/xenium_input -o /tmp/segger_293/segger_output --n-epochs 20 --prediction-expansion-ratio 0.5 --prediction-mode nucleus

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "/usr/local/bin/segger", line 6, in <module>
    sys.exit(app())
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/core.py", line 1947, in __call__
    result = _run_maybe_async_command(command, bound, resolved_backend)
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/_run.py", line 50, in _run_maybe_async_command
    return command(*bound.args, **bound.kwargs)
  File "/usr/local/lib/python3.12/dist-packages/segger/cli/segment.py", line 307, in segment
    from lightning.pytorch.plugins.environments import SLURMEnvironment
  File "/usr/local/lib/python3.12/dist-packages/lightning/__init__.py", line 18, in <module>
    from lightning.fabric.fabric import Fabric  # noqa: E402
  File "/usr/local/lib/python3.12/dist-packages/lightning/fabric/__init__.py", line 35, in <module>
    from lightning.fabric.fabric import Fabric  # noqa: E402
  File "/usr/local/lib/python3.12/dist-packages/lightning/fabric/fabric.py", line 30, in <module>
    import torch
  File "/usr/local/lib/python3.12/dist-packages/torch/__init__.py", line 2248, in <module>
    from torch import quantization as quantization  # usort: skip
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/__init__.py", line 2, in <module>
    from .fake_quantize import *  # noqa: F403
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/fake_quantize.py", line 10, in <module>
    from torch.ao.quantization.fake_quantize import (
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/__init__.py", line 12, in <module>
    from .pt2e._numeric_debugger import (  # noqa: F401
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/_numeric_debugger.py", line 9, in <module>
    from torch.ao.quantization.pt2e.graph_utils import bfs_trace_with_node_process
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/graph_utils.py", line 9, in <module>
    from torch.export import ExportedProgram
  File "/usr/local/lib/python3.12/dist-packages/torch/export/__init__.py", line 60, in <module>
    from .decomp_utils import CustomDecompTable
  File "/usr/local/lib/python3.12/dist-packages/torch/export/decomp_utils.py", line 5, in <module>
    from torch._export.utils import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/__init__.py", line 48, in <module>
    from .wrappers import _wrap_submodules
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/wrappers.py", line 7, in <module>
    from torch._higher_order_ops.flat_apply import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/__init__.py", line 1, in <module>
    from torch._higher_order_ops._invoke_quant import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/_invoke_quant.py", line 8, in <module>
    from torch._higher_order_ops.base_hop import BaseHOP, FunctionWithNoFreeVars
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/base_hop.py", line 12, in <module>
    from torch._subclasses.functional_tensor import disable_functional_mode
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 46, in <module>
    class FunctionalTensor(torch.Tensor):
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 279, in FunctionalTensor
    cpu = _conversion_method_template(device=torch.device("cpu"))
/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py:279: UserWarning: Failed to initialize NumPy: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

 (Triggered internally at /opt/pytorch/pytorch/torch/csrc/utils/tensor_numpy.cpp:81.)
  cpu = _conversion_method_template(device=torch.device("cpu"))
Traceback (most recent call last):
  File "/usr/local/bin/segger", line 6, in <module>
    sys.exit(app())
             ^^^^^
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/core.py", line 1947, in __call__
    result = _run_maybe_async_command(command, bound, resolved_backend)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/_run.py", line 50, in _run_maybe_async_command
    return command(*bound.args, **bound.kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/segger/cli/segment.py", line 313, in segment
    datamodule = ISTDataModule(
                 ^^^^^^^^^^^^^^
  File "<string>", line 27, in __init__
  File "/usr/local/lib/python3.12/dist-packages/segger/data/data_module.py", line 160, in __post_init__
    self.load()
  File "/usr/local/lib/python3.12/dist-packages/segger/data/data_module.py", line 173, in load
    bd = self.bd = pp.boundaries
                   ^^^^^^^^^^^^^
  File "/usr/lib/python3.12/functools.py", line 995, in __get__
    val = self.func(instance)
          ^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/segger/io/preprocessor.py", line 500, in boundaries
    bd.index = bd[std.id] + '_' + bd[std.boundary_type].map({
               ~~~~~~~~~~~^~~~~
  File "/usr/local/lib/python3.12/dist-packages/pandas/core/ops/common.py", line 76, in new_method
    return method(self, other)
           ^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/pandas/core/arraylike.py", line 186, in __add__
    return self._arith_method(other, operator.add)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/pandas/core/series.py", line 6154, in _arith_method
    return base.IndexOpsMixin._arith_method(self, other, op)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/pandas/core/base.py", line 1391, in _arith_method
    result = ops.arithmetic_op(lvalues, rvalues, op)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/pandas/core/ops/array_ops.py", line 283, in arithmetic_op
    res_values = _na_arithmetic_op(left, right, op)  # type: ignore[arg-type]
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/pandas/core/ops/array_ops.py", line 218, in _na_arithmetic_op
    result = func(left, right)
             ^^^^^^^^^^^^^^^^^
numpy._core._exceptions._UFuncNoLoopError: ufunc 'add' did not contain a loop with signature matching types (dtype('int64'), dtype('<U1')) -> None
Traceback (most recent call last):
  File "/scratch/2vU8vpPrOaSTxY/46/343393a7896a8c3116d8804591dec8/.viash_script.py", line 384, in <module>
    seg_pq = _run_segger(xenium_dir, segger_out_dir)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/scratch/2vU8vpPrOaSTxY/46/343393a7896a8c3116d8804591dec8/.viash_script.py", line 268, in _run_segger
    subprocess.run(cmd, check=True, env=env)
  File "/usr/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['segger', 'segment', '-i', '/tmp/segger_293/xenium_input', '-o', '/tmp/segger_293/segger_output', '--n-epochs', '20', '--prediction-expansion-ratio', '0.5', '--prediction-mode', 'nucleus']' returned non-zero exit status 1.
```

[rcannood]

/etc/bash.bashrc: line 9: PS1: unbound variable

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "/scratch/4OGfkR1QvsajoS/b8/892b3af2feaf3326905d40b18be643/.viash_script.py", line 12, in <module>
    import torch
  File "/usr/local/lib/python3.12/dist-packages/torch/__init__.py", line 2248, in <module>
    from torch import quantization as quantization  # usort: skip
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/__init__.py", line 2, in <module>
    from .fake_quantize import *  # noqa: F403
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/fake_quantize.py", line 10, in <module>
    from torch.ao.quantization.fake_quantize import (
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/__init__.py", line 12, in <module>
    from .pt2e._numeric_debugger import (  # noqa: F401
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/_numeric_debugger.py", line 9, in <module>
    from torch.ao.quantization.pt2e.graph_utils import bfs_trace_with_node_process
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/graph_utils.py", line 9, in <module>
    from torch.export import ExportedProgram
  File "/usr/local/lib/python3.12/dist-packages/torch/export/__init__.py", line 60, in <module>
    from .decomp_utils import CustomDecompTable
  File "/usr/local/lib/python3.12/dist-packages/torch/export/decomp_utils.py", line 5, in <module>
    from torch._export.utils import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/__init__.py", line 48, in <module>
    from .wrappers import _wrap_submodules
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/wrappers.py", line 7, in <module>
    from torch._higher_order_ops.flat_apply import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/__init__.py", line 1, in <module>
    from torch._higher_order_ops._invoke_quant import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/_invoke_quant.py", line 8, in <module>
    from torch._higher_order_ops.base_hop import BaseHOP, FunctionWithNoFreeVars
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/base_hop.py", line 12, in <module>
    from torch._subclasses.functional_tensor import disable_functional_mode
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 46, in <module>
    class FunctionalTensor(torch.Tensor):
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 279, in FunctionalTensor
    cpu = _conversion_method_template(device=torch.device("cpu"))
/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py:279: UserWarning: Failed to initialize NumPy: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

 (Triggered internally at /opt/pytorch/pytorch/torch/csrc/utils/tensor_numpy.cpp:81.)
  cpu = _conversion_method_template(device=torch.device("cpu"))
Using device: cuda
Reading input: _viash_par/input_1/spatial_unlabelled.zarr
Input:  SpatialData object, with associated Zarr store: /scratch/4OGfkR1QvsajoS/stage-b0f825cd-5643-470d-a1b1-a8d22f9f5ada/82/f20f2680f607ccd04cff75312df1f8/spatial_unlabelled.zarr
├── Images
│     └── 'image': DataTree[cyx] (1, 1000, 1000), (1, 500, 500), (1, 250, 250), (1, 125, 125), (1, 62, 62)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (1000, 1000), (500, 500), (250, 250), (125, 125), (62, 62)
│     └── 'nucleus_labels': DataTree[yx] (1000, 1000), (500, 500), (250, 250), (125, 125), (62, 62)
├── Points
│     └── 'transcripts': DataFrame with shape: (<Delayed>, 8) (3D points)
└── Tables
      └── 'table': AnnData (0, 424)
with coordinate systems:
    ▸ 'global', with elements:
        image (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points)
Init segmentation mode: transcript_cell_id
Initial segmentation: 307 polygons
Running segger: segger segment -i /tmp/segger_276/xenium_input -o /tmp/segger_276/segger_output --n-epochs 20 --prediction-expansion-ratio 0.5 --prediction-mode nucleus

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "/usr/local/bin/segger", line 6, in <module>
    sys.exit(app())
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/core.py", line 1947, in __call__
    result = _run_maybe_async_command(command, bound, resolved_backend)
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/_run.py", line 50, in _run_maybe_async_command
    return command(*bound.args, **bound.kwargs)
  File "/usr/local/lib/python3.12/dist-packages/segger/cli/segment.py", line 307, in segment
    from lightning.pytorch.plugins.environments import SLURMEnvironment
  File "/usr/local/lib/python3.12/dist-packages/lightning/__init__.py", line 18, in <module>
    from lightning.fabric.fabric import Fabric  # noqa: E402
  File "/usr/local/lib/python3.12/dist-packages/lightning/fabric/__init__.py", line 35, in <module>
    from lightning.fabric.fabric import Fabric  # noqa: E402
  File "/usr/local/lib/python3.12/dist-packages/lightning/fabric/fabric.py", line 30, in <module>
    import torch
  File "/usr/local/lib/python3.12/dist-packages/torch/__init__.py", line 2248, in <module>
    from torch import quantization as quantization  # usort: skip
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/__init__.py", line 2, in <module>
    from .fake_quantize import *  # noqa: F403
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/fake_quantize.py", line 10, in <module>
    from torch.ao.quantization.fake_quantize import (
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/__init__.py", line 12, in <module>
    from .pt2e._numeric_debugger import (  # noqa: F401
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/_numeric_debugger.py", line 9, in <module>
    from torch.ao.quantization.pt2e.graph_utils import bfs_trace_with_node_process
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/graph_utils.py", line 9, in <module>
    from torch.export import ExportedProgram
  File "/usr/local/lib/python3.12/dist-packages/torch/export/__init__.py", line 60, in <module>
    from .decomp_utils import CustomDecompTable
  File "/usr/local/lib/python3.12/dist-packages/torch/export/decomp_utils.py", line 5, in <module>
    from torch._export.utils import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/__init__.py", line 48, in <module>
    from .wrappers import _wrap_submodules
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/wrappers.py", line 7, in <module>
    from torch._higher_order_ops.flat_apply import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/__init__.py", line 1, in <module>
    from torch._higher_order_ops._invoke_quant import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/_invoke_quant.py", line 8, in <module>
    from torch._higher_order_ops.base_hop import BaseHOP, FunctionWithNoFreeVars
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/base_hop.py", line 12, in <module>
    from torch._subclasses.functional_tensor import disable_functional_mode
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 46, in <module>
    class FunctionalTensor(torch.Tensor):
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 279, in FunctionalTensor
    cpu = _conversion_method_template(device=torch.device("cpu"))
/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py:279: UserWarning: Failed to initialize NumPy: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

 (Triggered internally at /opt/pytorch/pytorch/torch/csrc/utils/tensor_numpy.cpp:81.)
  cpu = _conversion_method_template(device=torch.device("cpu"))
Traceback (most recent call last):
  File "/usr/local/bin/segger", line 6, in <module>
    sys.exit(app())
             ^^^^^
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/core.py", line 1947, in __call__
    result = _run_maybe_async_command(command, bound, resolved_backend)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/_run.py", line 50, in _run_maybe_async_command
    return command(*bound.args, **bound.kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/segger/cli/segment.py", line 313, in segment
    datamodule = ISTDataModule(
                 ^^^^^^^^^^^^^^
  File "<string>", line 27, in __init__
  File "/usr/local/lib/python3.12/dist-packages/segger/data/data_module.py", line 160, in __post_init__
    self.load()
  File "/usr/local/lib/python3.12/dist-packages/segger/data/data_module.py", line 195, in load
    self.ad = setup_anndata(
              ^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/segger/data/utils/anndata.py", line 150, in setup_anndata
    ad = anndata_from_transcripts(
         ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/segger/data/utils/anndata.py", line 58, in anndata_from_transcripts
    X = sp.coo_matrix((ijv[2], ijv[:2])).tocsr()
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/scipy/sparse/_coo.py", line 52, in __init__
    raise ValueError('cannot infer dimensions from zero '
ValueError: cannot infer dimensions from zero sized index arrays
Traceback (most recent call last):
  File "/scratch/4OGfkR1QvsajoS/b8/892b3af2feaf3326905d40b18be643/.viash_script.py", line 390, in <module>
    seg_pq = _run_segger(xenium_dir, segger_out_dir)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/scratch/4OGfkR1QvsajoS/b8/892b3af2feaf3326905d40b18be643/.viash_script.py", line 274, in _run_segger
    subprocess.run(cmd, check=True, env=env)
  File "/usr/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['segger', 'segment', '-i', '/tmp/segger_276/xenium_input', '-o', '/tmp/segger_276/segger_output', '--n-epochs', '20', '--prediction-expansion-ratio', '0.5', '--prediction-mode', 'nucleus']' returned non-zero exit status 1.

[rcannood]

---

root@debug-segger:/scratch/4OGfkR1QvsajoS/b8/892b3af2feaf3326905d40b18be643# python .viash_script.py 

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "/scratch/4OGfkR1QvsajoS/b8/892b3af2feaf3326905d40b18be643/.viash_script.py", line 12, in <module>
    import torch
  File "/usr/local/lib/python3.12/dist-packages/torch/__init__.py", line 2248, in <module>
    from torch import quantization as quantization  # usort: skip
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/__init__.py", line 2, in <module>
    from .fake_quantize import *  # noqa: F403
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/fake_quantize.py", line 10, in <module>
    from torch.ao.quantization.fake_quantize import (
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/__init__.py", line 12, in <module>
    from .pt2e._numeric_debugger import (  # noqa: F401
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/_numeric_debugger.py", line 9, in <module>
    from torch.ao.quantization.pt2e.graph_utils import bfs_trace_with_node_process
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/graph_utils.py", line 9, in <module>
    from torch.export import ExportedProgram
  File "/usr/local/lib/python3.12/dist-packages/torch/export/__init__.py", line 60, in <module>
    from .decomp_utils import CustomDecompTable
  File "/usr/local/lib/python3.12/dist-packages/torch/export/decomp_utils.py", line 5, in <module>
    from torch._export.utils import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/__init__.py", line 48, in <module>
    from .wrappers import _wrap_submodules
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/wrappers.py", line 7, in <module>
    from torch._higher_order_ops.flat_apply import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/__init__.py", line 1, in <module>
    from torch._higher_order_ops._invoke_quant import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/_invoke_quant.py", line 8, in <module>
    from torch._higher_order_ops.base_hop import BaseHOP, FunctionWithNoFreeVars
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/base_hop.py", line 12, in <module>
    from torch._subclasses.functional_tensor import disable_functional_mode
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 46, in <module>
    class FunctionalTensor(torch.Tensor):
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 279, in FunctionalTensor
    cpu = _conversion_method_template(device=torch.device("cpu"))
/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py:279: UserWarning: Failed to initialize NumPy: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

 (Triggered internally at /opt/pytorch/pytorch/torch/csrc/utils/tensor_numpy.cpp:81.)
  cpu = _conversion_method_template(device=torch.device("cpu"))
Using device: cuda
Reading input: _viash_par/input_1/spatial_unlabelled.zarr
Input:  SpatialData object, with associated Zarr store: /scratch/4OGfkR1QvsajoS/stage-b0f825cd-5643-470d-a1b1-a8d22f9f5ada/82/f20f2680f607ccd04cff75312df1f8/spatial_unlabelled.zarr
├── Images
│     └── 'image': DataTree[cyx] (1, 1000, 1000), (1, 500, 500), (1, 250, 250), (1, 125, 125), (1, 62, 62)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (1000, 1000), (500, 500), (250, 250), (125, 125), (62, 62)
│     └── 'nucleus_labels': DataTree[yx] (1000, 1000), (500, 500), (250, 250), (125, 125), (62, 62)
├── Points
│     └── 'transcripts': DataFrame with shape: (<Delayed>, 8) (3D points)
└── Tables
      └── 'table': AnnData (0, 424)
with coordinate systems:
    ▸ 'global', with elements:
        image (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points)
Init segmentation mode: transcript_cell_id
Initial segmentation: 307 polygons
transcripts.parquet: 68940/69101 assigned across 309 cells
Running segger: segger segment -i /tmp/segger_2801/xenium_input -o /tmp/segger_2801/segger_output --n-epochs 20 --prediction-expansion-ratio 0.5 --prediction-mode nucleus

A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last):  File "/usr/local/bin/segger", line 6, in <module>
    sys.exit(app())
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/core.py", line 1947, in __call__
    result = _run_maybe_async_command(command, bound, resolved_backend)
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/_run.py", line 50, in _run_maybe_async_command
    return command(*bound.args, **bound.kwargs)
  File "/usr/local/lib/python3.12/dist-packages/segger/cli/segment.py", line 307, in segment
    from lightning.pytorch.plugins.environments import SLURMEnvironment
  File "/usr/local/lib/python3.12/dist-packages/lightning/__init__.py", line 18, in <module>
    from lightning.fabric.fabric import Fabric  # noqa: E402
  File "/usr/local/lib/python3.12/dist-packages/lightning/fabric/__init__.py", line 35, in <module>
    from lightning.fabric.fabric import Fabric  # noqa: E402
  File "/usr/local/lib/python3.12/dist-packages/lightning/fabric/fabric.py", line 30, in <module>
    import torch
  File "/usr/local/lib/python3.12/dist-packages/torch/__init__.py", line 2248, in <module>
    from torch import quantization as quantization  # usort: skip
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/__init__.py", line 2, in <module>
    from .fake_quantize import *  # noqa: F403
  File "/usr/local/lib/python3.12/dist-packages/torch/quantization/fake_quantize.py", line 10, in <module>
    from torch.ao.quantization.fake_quantize import (
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/__init__.py", line 12, in <module>
    from .pt2e._numeric_debugger import (  # noqa: F401
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/_numeric_debugger.py", line 9, in <module>
    from torch.ao.quantization.pt2e.graph_utils import bfs_trace_with_node_process
  File "/usr/local/lib/python3.12/dist-packages/torch/ao/quantization/pt2e/graph_utils.py", line 9, in <module>
    from torch.export import ExportedProgram
  File "/usr/local/lib/python3.12/dist-packages/torch/export/__init__.py", line 60, in <module>
    from .decomp_utils import CustomDecompTable
  File "/usr/local/lib/python3.12/dist-packages/torch/export/decomp_utils.py", line 5, in <module>
    from torch._export.utils import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/__init__.py", line 48, in <module>
    from .wrappers import _wrap_submodules
  File "/usr/local/lib/python3.12/dist-packages/torch/_export/wrappers.py", line 7, in <module>
    from torch._higher_order_ops.flat_apply import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/__init__.py", line 1, in <module>
    from torch._higher_order_ops._invoke_quant import (
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/_invoke_quant.py", line 8, in <module>
    from torch._higher_order_ops.base_hop import BaseHOP, FunctionWithNoFreeVars
  File "/usr/local/lib/python3.12/dist-packages/torch/_higher_order_ops/base_hop.py", line 12, in <module>
    from torch._subclasses.functional_tensor import disable_functional_mode
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 46, in <module>
    class FunctionalTensor(torch.Tensor):
  File "/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py", line 279, in FunctionalTensor
    cpu = _conversion_method_template(device=torch.device("cpu"))
/usr/local/lib/python3.12/dist-packages/torch/_subclasses/functional_tensor.py:279: UserWarning: Failed to initialize NumPy: 
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.2.6 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.

 (Triggered internally at /opt/pytorch/pytorch/torch/csrc/utils/tensor_numpy.cpp:81.)
  cpu = _conversion_method_template(device=torch.device("cpu"))
Traceback (most recent call last):
  File "/usr/local/bin/segger", line 6, in <module>
    sys.exit(app())
             ^^^^^
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/core.py", line 1947, in __call__
    result = _run_maybe_async_command(command, bound, resolved_backend)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/cyclopts/_run.py", line 50, in _run_maybe_async_command
    return command(*bound.args, **bound.kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/segger/cli/segment.py", line 313, in segment
    datamodule = ISTDataModule(
                 ^^^^^^^^^^^^^^
  File "<string>", line 27, in __init__
  File "/usr/local/lib/python3.12/dist-packages/segger/data/data_module.py", line 160, in __post_init__
    self.load()
  File "/usr/local/lib/python3.12/dist-packages/segger/data/data_module.py", line 195, in load
    self.ad = setup_anndata(
              ^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/segger/data/utils/anndata.py", line 173, in setup_anndata
    assert ~ad.obs.index.isna().any()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError
Traceback (most recent call last):
  File "/scratch/4OGfkR1QvsajoS/b8/892b3af2feaf3326905d40b18be643/.viash_script.py", line 453, in <module>
    seg_pq = _run_segger(xenium_dir, segger_out_dir)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/scratch/4OGfkR1QvsajoS/b8/892b3af2feaf3326905d40b18be643/.viash_script.py", line 298, in _run_segger
    subprocess.run(cmd, check=True, env=env)
  File "/usr/lib/python3.12/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['segger', 'segment', '-i', '/tmp/segger_2801/xenium_input', '-o', '/tmp/segger_2801/segger_output', '--n-epochs', '20', '--prediction-expansion-ratio', '0.5', '--prediction-mode', 'nucleus']' returned non-zero exit status 1.
root@debug-segger:/scratch/4OGfkR1QvsajoS/b8/892b3af2feaf3326905d40b18be643#