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verified publisher icon khanlab

Pb Chimpanzee data application

Open MaeligChauvel opened this issue 9 months ago • 9 comments

Command used : singularity run -e khanlab_hippunfold_1.5.1.sif TryChimpanzeedata OutputTestFolder participant --modality T1w --cores 20 --rigid-reg-template --skip-inject-template-labels

Error message :

Config file config/snakebids.yml is extended by additional config specified via the command line. Building DAG of jobs... Using shell: /bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Singularity containers: ignored Job stats: job count

affine_gii_to_native 6 all 1 archive_work_after_final 1 calculate_curvature_from_surface1 2 calculate_curvature_from_surface2 2 calculate_gyrification1 2 calculate_gyrification2 2 calculate_surface_area1 2 calculate_surface_area2 2 calculate_thickness_from_surface1 2 calculate_thickness_from_surface2 2 combine_tissue_subfield_labels_corobl 2 compose_warps_native_to_unfold 2 compose_warps_unfold_to_crop_native 2 correct_nan_vertices1 6 correct_nan_vertices2 6 cp_unfolded_noconstrain 2 create_dscalar_metric_cifti 3 create_native_coord_ref 2 create_native_crop_ref 2 create_spec_file_hipp 2 create_warps_hipp 2 equivolume_coords 2 expand_unfolded_warps 4 get_subfield_vols_subj 1 label_subfields_from_vol_coords_corobl 2 laplace_coords_hipp 6 merge_lr_spec_file 1 metric_to_nii 6 normalize_curvature1 2 normalize_curvature2 2 plot_subj_subfields 1 qc_subfield 2 qc_subfield_surf 2 resample_coords_native_crop 8 resample_native_to_crop 2 resample_subfields_native_crop 2 resample_subfields_to_native 2 resample_unfoldreg_subfields 2 unfolded_registration 2 warp_gii_unfold2corobl1 6 warp_gii_unfold2corobl2 6 warp_gii_unfoldreg 6 total 122

Select jobs to execute...

[Tue Mar 18 15:48:37 2025] rule laplace_coords_hipp: input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-PD_hemi-L_laplace-hipp.txt jobid: 24 reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz wildcards: subject=Jimmy, dir=PD, hemi=L resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025] rule laplace_coords_hipp: input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-AP_hemi-R_laplace-hipp.txt jobid: 79 reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz wildcards: subject=Jimmy, dir=AP, hemi=R resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025] rule laplace_coords_hipp: input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-L_laplace-hipp.txt jobid: 149 reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz wildcards: subject=Jimmy, dir=IO, hemi=L resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025] rule equivolume_coords: input: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-all_mask.nii.gz, work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-SRLM_mask.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-R_equivolume.txt jobid: 83 reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz wildcards: subject=Jimmy, dir=IO, hemi=R resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025] rule laplace_coords_hipp: input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-R_laplace-hipp.txt jobid: 151 reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz wildcards: subject=Jimmy, dir=IO, hemi=R resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025] rule equivolume_coords: input: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-all_mask.nii.gz, work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-SRLM_mask.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-L_equivolume.txt jobid: 25 reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz wildcards: subject=Jimmy, dir=IO, hemi=L resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025] rule laplace_coords_hipp: input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-AP_hemi-L_laplace-hipp.txt jobid: 12 reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz wildcards: subject=Jimmy, dir=AP, hemi=L resources: tmpdir=/tmp, time=30

[Tue Mar 18 15:48:37 2025] rule laplace_coords_hipp: input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-PD_hemi-R_laplace-hipp.txt jobid: 82 reason: Missing output files: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz wildcards: subject=Jimmy, dir=PD, hemi=R resources: tmpdir=/tmp, time=30

/opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0 warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}" /opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0 warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}" /opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0 warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}" /opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0 warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}" /opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0 warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}" /opt/conda/lib/python3.9/site-packages/scipy/init.py:146: UserWarning: A NumPy version >=1.16.5 and <1.23.0 is required for this version of SciPy (detected version 1.26.0 warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}" Traceback (most recent call last): Traceback (most recent call last): File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmpbi7_agqc.laplace_coords.py", line 8, in File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmp8gp7sng2.laplace_coords.py", line 8, in Traceback (most recent call last): File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmpwlqp024h.laplace_coords.py", line 8, in from astropy.convolution import convolve as nan_convolve File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in Traceback (most recent call last): from astropy.convolution import convolve as nan_convolve from astropy.convolution import convolve as nan_convolve File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmprm5jlijt.laplace_coords.py", line 8, in File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in from astropy.convolution import convolve as nan_convolve File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in from .core import * # noqa File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in from .core import * # noqa File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in from .core import * # noqa File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in from .core import * # noqa File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in from .utils import (discretize_model, add_kernel_arrays_1D, from .utils import (discretize_model, add_kernel_arrays_1D, from .utils import (discretize_model, add_kernel_arrays_1D, File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in from .utils import (discretize_model, add_kernel_arrays_1D, File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in Traceback (most recent call last): File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmp6i9ei5j7.laplace_coords.py", line 8, in from astropy.convolution import convolve as nan_convolve File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in from .core import * # noqa File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in from astropy.modeling.core import FittableModel, custom_model from astropy.modeling.core import FittableModel, custom_model from astropy.modeling.core import FittableModel, custom_model File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in from .utils import (discretize_model, add_kernel_arrays_1D, File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in from astropy.modeling.core import FittableModel, custom_model File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in from astropy.modeling.core import FittableModel, custom_model File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in from . import fitting from . import fitting from . import fitting from . import fitting File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in from . import fitting File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in Traceback (most recent call last): File "/data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmph24aoyid.laplace_coords.py", line 8, in from astropy.units import Quantity File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in from astropy.units import Quantity from astropy.units import Quantity File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in from astropy.units import Quantity File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in from astropy.units import Quantity File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in from astropy.convolution import convolve as nan_convolve File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/init.py", line 4, in from .core import * # noqa File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/core.py", line 23, in from .utils import (discretize_model, add_kernel_arrays_1D, File "/opt/conda/lib/python3.9/site-packages/astropy/convolution/utils.py", line 5, in from astropy.modeling.core import FittableModel, custom_model File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/init.py", line 10, in from . import fitting File "/opt/conda/lib/python3.9/site-packages/astropy/modeling/fitting.py", line 39, in from .quantity import * from .quantity import * from .quantity import * from .quantity import * File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in from astropy.units import Quantity File "/opt/conda/lib/python3.9/site-packages/astropy/units/init.py", line 17, in from .quantity import * File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in from .quantity import * File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity.py", line 28, in from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit, from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit, File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit, File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit, File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit, File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in from .quantity_helper import (converters_and_unit, can_have_arbitrary_unit, File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/init.py", line 10, in from . import helpers, function_helpers from . import helpers, function_helpers from . import helpers, function_helpers File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in from . import helpers, function_helpers from . import helpers, function_helpers from . import helpers, function_helpers File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in File "/opt/conda/lib/python3.9/site-packages/astropy/units/quantity_helper/function_helpers.py", line 119, in np.asscalar, np.asscalar, np.asscalar, File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr np.asscalar, np.asscalar, File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr np.asscalar, File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'asscalar' raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'asscalar' raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'asscalar' raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'asscalar' raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'asscalar' raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'asscalar' [Tue Mar 18 15:48:38 2025] Error in rule laplace_coords_hipp: jobid: 149 input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-L_laplace-hipp.txt (check log file(s) for error details)

[Tue Mar 18 15:48:38 2025] [Tue Mar 18 15:48:38 2025] Error in rule laplace_coords_hipp: jobid: 151 input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-R_laplace-hipp.txt (check log file(s) for error details)

Error in rule laplace_coords_hipp: jobid: 24 input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-PD_hemi-L_laplace-hipp.txt (check log file(s) for error details)

[Tue Mar 18 15:48:38 2025] Error in rule laplace_coords_hipp: jobid: 79 input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-AP_hemi-R_laplace-hipp.txt (check log file(s) for error details)

RuleException: CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84: Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmpwlqp024h.laplace_coords.py' returned non-zero exit status 1. File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run RuleException: CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84: Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmpbi7_agqc.laplace_coords.py' returned non-zero exit status 1. File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run RuleException: CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84: Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmp8gp7sng2.laplace_coords.py' returned non-zero exit status 1. File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run [Tue Mar 18 15:48:38 2025] Error in rule laplace_coords_hipp: jobid: 12 input: work/sub-Jimmy/anat/sub-Jimmy_hemi-L_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-AP_hemi-L_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-AP_hemi-L_laplace-hipp.txt (check log file(s) for error details)

RuleException: CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84: Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmp6i9ei5j7.laplace_coords.py' returned non-zero exit status 1. File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run RuleException: CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84: Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmph24aoyid.laplace_coords.py' returned non-zero exit status 1. File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run [Tue Mar 18 15:48:38 2025] Error in rule laplace_coords_hipp: jobid: 82 input: work/sub-Jimmy/anat/sub-Jimmy_hemi-R_space-corobl_desc-nnunet_dseg.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-PD_hemi-R_space-corobl_label-hipp_desc-laplace_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-PD_hemi-R_laplace-hipp.txt (check log file(s) for error details)

RuleException: CalledProcessError in file /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk, line 84: Command 'set -euo pipefail; /opt/conda/bin/python /data/pt_02101/Hippocampus/Try_hippunfold/MaeligTestFolder/.snakemake/scripts/tmprm5jlijt.laplace_coords.py' returned non-zero exit status 1. File "/opt/conda/lib/python3.9/site-packages/hippunfold/workflow/rules/autotop.smk", line 84, in __rule_laplace_coords_hipp File "/opt/conda/lib/python3.9/concurrent/futures/thread.py", line 52, in run [Tue Mar 18 15:48:44 2025] Error in rule equivolume_coords: jobid: 83 input: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-all_mask.nii.gz, work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-SRLM_mask.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-R_equivolume.txt (check log file(s) for error details) shell: python /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/scripts/equivolume_coords.py /tmp work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-SRLM_mask.nii.gz work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_desc-all_mask.nii.gz work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-R_space-corobl_label-hipp_desc-equivol_coords.nii.gz &> logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-R_equivolume.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue Mar 18 15:48:44 2025] Error in rule equivolume_coords: jobid: 25 input: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-all_mask.nii.gz, work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-SRLM_mask.nii.gz output: work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz log: logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-L_equivolume.txt (check log file(s) for error details) shell: python /opt/conda/lib/python3.9/site-packages/hippunfold/workflow/scripts/equivolume_coords.py /tmp work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-SRLM_mask.nii.gz work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_desc-all_mask.nii.gz work/sub-Jimmy/coords/sub-Jimmy_dir-IO_hemi-L_space-corobl_label-hipp_desc-equivol_coords.nii.gz &> logs/sub-Jimmy/sub-Jimmy_dir-IO_hemi-L_equivolume.txt (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-03-18T154835.359670.snakemake.log

MaeligChauvel avatar Mar 18 '25 14:03 MaeligChauvel

another quick note from our conversation today: we tried with & without template shape injection, the error is the same. There are likely two issues:

  1. the segmentation is not correct because we are using chimpanzee data here with a human (and also tried marmoset) nnunet/registration. But I dont think this would throw an error, just give bad results.
  2. this specific error message seems to be caused by an issue with astropy. I wonder if we've accidentally broken our dependencies somewhere...

jordandekraker avatar Mar 18 '25 16:03 jordandekraker

No, it looks like like the problem is stemming from the local python environment getting picked up and having conflicts:

File "/data/hu_chauvel/.local/lib/python3.9/site-packages/numpy/init.py", line 333, in getattr

My recommendation is to remove any python packages from your ~/.local/lib path (it is not recommended to put things there directly anyways).. you might be able to work around by altering your singularity bind paths too, but I would just suggest clearing it out (and using something like virtualenv, pipx or uvx for those things you had installed there..)

akhanf avatar Mar 18 '25 17:03 akhanf

Yes it sounds like that should work, but I'm surprised that singularity includes ~/.local/lib in its path, since the singularity -e flag is being used. This makes me worry that singularity might not be quite as isolating as I'd hoped. I wonder if there's something we can include in the Dockerfile to avoid this issue?

jordandekraker avatar Mar 20 '25 13:03 jordandekraker

Recall that the -e flag only clears the environment variables, ie it doesn't control what is on your filesystem. If python sees ~/.local/lib/ it tries to look for packages there..

akhanf avatar Mar 20 '25 14:03 akhanf

Ie it is not coming from the environment variables but from the files on the filesystem

akhanf avatar Mar 20 '25 14:03 akhanf

Seems like a quick fix would be to add PYTHONNOUSERSITE to the Dockerfile https://stackoverflow.com/questions/41360022/how-to-ignore-python-module-in-local-lib-python2-7-site-packages

jordandekraker avatar Mar 20 '25 14:03 jordandekraker

ah didn't know about that env var -- yes can be set in the dockerfile -- ~note you would also have to set SINGULARITYENV_PYTHONNOUSERSITE (and for future-proofing maybe: APPTAINERENV_PYTHONNOUSERSITE)~ (nevermind that would only be for --use-singularity cases..)

akhanf avatar Mar 20 '25 14:03 akhanf

just looping back so we can close this if possible -- did this correct the issue @MaeligChauvel ?

akhanf avatar Apr 17 '25 14:04 akhanf

Hi,

I need to check what I can do on my side, please don't close it for now.

Best regards,

Maelig

De : Ali Khan @.> Envoyé : jeudi 17 avril 2025 14:30 À : khanlab/hippunfold @.> Cc : Maelig Chauvel @.>; Mention @.> Objet : Re: [khanlab/hippunfold] Pb Chimpanzee data application (Issue #400)

just looping back so we can close this if possible -- did this correct the issue @MaeligChauvelhttps://github.com/MaeligChauvel ?

— Reply to this email directly, view it on GitHubhttps://github.com/khanlab/hippunfold/issues/400#issuecomment-2813133761, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BI65DFMPAHUR4QTOBJ6RBTD2Z63J7AVCNFSM6AAAAABZIMF23OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQMJTGEZTGNZWGE. You are receiving this because you were mentioned.Message ID: @.***>

[https://avatars.githubusercontent.com/u/11492701?s=20&v=4]akhanf left a comment (khanlab/hippunfold#400)https://github.com/khanlab/hippunfold/issues/400#issuecomment-2813133761

just looping back so we can close this if possible -- did this correct the issue @MaeligChauvelhttps://github.com/MaeligChauvel ?

— Reply to this email directly, view it on GitHubhttps://github.com/khanlab/hippunfold/issues/400#issuecomment-2813133761, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BI65DFMPAHUR4QTOBJ6RBTD2Z63J7AVCNFSM6AAAAABZIMF23OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQMJTGEZTGNZWGE. You are receiving this because you were mentioned.Message ID: @.***>

MaeligChauvel avatar Apr 17 '25 15:04 MaeligChauvel