C-PAC v1.7.0 - brainlife app

C-PAC Run Info


Description	debugging C-PAC brainlife app
Version	v1.7.0
Container	Singularity 2.5.2
System	local Debian
Data Size	63 × 82 × 50 × 188
Results	2 crashfiles: `crash-20200811-151414-jon-check_for_s3.b0-bf6796fa-60c1-46f3-84ef-f66e049501e5.pklz` `crash-20200811-151514-jon-check_for_s3-0cbfca44-3765-4974-b860-6febf4613281.pklz`

`crash-20200811-151414-jon-check_for_s3.b0-bf6796fa-60c1-46f3-84ef-f66e049501e5.pklz`

Nipype version 1.1.2
Traceback (most recent call last):

  File "/home/jon/.local/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)

  File "/home/jon/.local/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)

  File "/home/jon/.local/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)

  File "/home/jon/.local/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)

  File "/home/jon/.local/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 521, in run
    runtime = self._run_interface(runtime)

  File "/code/CPAC/utils/interfaces/function.py", line 152, in _run_interface
    out = function_handle(**args)

  File "/code/CPAC/utils/datasource.py", line 490, in check_for_s3
    raise IOError('File {0} does not exist!'.format(local_path))

OSError: File bids/sub-9002/ses-1/func/sub-9002_ses-1_task-rest_bold.nii.gz does not exist!

`crash-20200811-151514-jon-check_for_s3-0cbfca44-3765-4974-b860-6febf4613281.pklz`

Nipype version 1.1.2
Traceback (most recent call last):

  File "/home/jon/.local/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)

  File "/home/jon/.local/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)

  File "/home/jon/.local/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)

  File "/home/jon/.local/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)

  File "/home/jon/.local/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 521, in run
    runtime = self._run_interface(runtime)

  File "/code/CPAC/utils/interfaces/function.py", line 152, in _run_interface
    out = function_handle(**args)

  File "/code/CPAC/utils/datasource.py", line 490, in check_for_s3
    raise IOError('File {0} does not exist!'.format(local_path))

OSError: File bids/sub-9002/ses-1/anat/sub-9002_ses-1_T1w.nii.gz does not exist!

It seems os.path.exists does not follow symlinks:

$ stat bids/sub-9002/ses-1/func/sub-9002_ses-1_task-rest_bold.nii.gz
  File: bids/sub-9002/ses-1/func/sub-9002_ses-1_task-rest_bold.nii.gz -> ../5f31a85fa5b6433f55a4dec1/5e546c4b5b9d90232672dae5/bold.nii.gz
  Size: 64          Blocks: 8          IO Block: 4096   symbolic link

$ stat ../5f31a85fa5b6433f55a4dec1/5e546c4b5b9d90232672dae5/bold.nii.gz 
  File: ../5f31a85fa5b6433f55a4dec1/5e546c4b5b9d90232672dae5/bold.nii.gz
  Size: 159368742   Blocks: 311280     IO Block: 4096   regular file

>>> os.path.exists("../5f31a85fa5b6433f55a4dec1/5e546c4b5b9d90232672dae5/bold.nii.gz")
True
>>> os.path.exists("bids/sub-9002/ses-1/func/sub-9002_ses-1_task-rest_bold.nii.gz")
False
>>> os.path.lexists("bids/sub-9002/ses-1/func/sub-9002_ses-1_task-rest_bold.nii.gz")
True

Include:

[x] Run Command:


./main

[x] Pipeline Config: default pipeline
[x] Data Config: config.json via bl2bids
[ ] Screenshots of brain extraction and registration wireframe overlays from QC pages (if available):


N/A

[x] Node timing information:


('resting_preproc_sub-9002_ses-1.montage_sca_tempreg_maps_files_smooth_0.resample_u', 2.0)

('resting_preproc_sub-9002_ses-1.montage_sca_tempreg_maps_zstat_files_smooth_0.resample_u', 2.0) ('resting_preproc_sub-9002_ses-1.montage_alff_to_standard_zstd_0.resample_u', 2.0) ('resting_preproc_sub-9002_ses-1.montage_alff_to_standard_1.resample_u', 2.0) ('resting_preproc_sub-9002_ses-1.func_gather_0.select_scan_params', 1.0) ('resting_preproc_sub-9002_ses-1.func_gather_0.selectrest', 1.0) ('resting_preproc_sub-9002_ses-1.func_gather_0.check_func_scan', 1.0) ('resting_preproc_sub-9002_ses-1.func_gather_0.s3_scan_params', 1.0) ('resting_preproc_sub-9002_ses-1.spatial_map_dataflow_0.check_for_s3', 1.0) ('resting_preproc_sub-9002_ses-1.spatial_map_dataflow_for_DR_1.check_for_s3', 1.0) ('resting_preproc_sub-9002_ses-1.resampled_template_brain_for_func_derivative', 1.0) ('resting_preproc_sub-9002_ses-1.resampled_template_brain_for_func_preproc', 1.0) ('resting_preproc_sub-9002_ses-1.resampled_template_skull_for_func_derivative', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_tempreg_maps_files_smooth_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_tempreg_maps_zstat_files_smooth_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_tempreg_maps_files_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_tempreg_maps_zstat_files_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_tempreg_maps_files_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_tempreg_maps_zstat_files_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_alff_to_standard_smooth_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_alff_to_standard_smooth_zstd_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_dr_tempreg_maps_files_to_standard_smooth_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_dr_tempreg_maps_zstat_files_to_standard_smooth_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_falff_to_standard_smooth_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_falff_to_standard_smooth_zstd_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_reho_to_standard_smooth_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_reho_to_standard_smooth_zstd_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_roi_files_to_standard_smooth_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_roi_files_to_standard_smooth_fisher_zstd_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_alff_to_standard_smooth_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_alff_to_standard_smooth_zstd_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_dr_tempreg_maps_files_to_standard_smooth_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_dr_tempreg_maps_zstat_files_to_standard_smooth_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_falff_to_standard_smooth_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_falff_to_standard_smooth_zstd_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_reho_to_standard_smooth_zstd_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_roi_files_to_standard_smooth_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_reho_to_standard_smooth_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_roi_files_to_standard_smooth_fisher_zstd_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_reho_to_standard_zstd_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_falff_to_standard_zstd_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_alff_to_standard_zstd_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_reho_to_standard_zstd_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_falff_to_standard_zstd_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_dr_tempreg_maps_files_to_standard_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_dr_tempreg_maps_zstat_files_to_standard_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_roi_files_to_standard_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_roi_files_to_standard_fisher_zstd_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_centrality_smooth_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_centrality_smooth_zstd_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_centrality_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_centrality_zstd_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_dr_tempreg_maps_files_to_standard_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_dr_tempreg_maps_zstat_files_to_standard_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_roi_files_to_standard_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_sca_roi_files_to_standard_fisher_zstd_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_centrality_smooth_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_centrality_smooth_zstd_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_centrality_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_centrality_zstd_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_vmhc_raw_score_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_vmhc_raw_score_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_alff_to_standard_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_falff_to_standard_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_reho_to_standard_0.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_falff_to_standard_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.montage_reho_to_standard_1.resample_u', 1.0) ('resting_preproc_sub-9002_ses-1.func_template_edge_1', 1.0) ('resting_preproc_sub-9002_ses-1.func_template_edge_0', 1.0) ('resting_preproc_sub-9002_ses-1.montage_mfi_1.resample_o', 1.0) ('resting_preproc_sub-9002_ses-1.montage_mfi_0.resample_o', 1.0) ('resting_preproc_sub-9002_ses-1.check_for_s3_PRIORS_WHITE', 1.0) ('resting_preproc_sub-9002_ses-1.check_for_s3_PRIORS_GRAY', 1.0) ('resting_preproc_sub-9002_ses-1.check_for_s3_PRIORS_CSF', 1.0) ('resting_preproc_sub-9002_ses-1.anat_template_edge_1', 1.0) ('resting_preproc_sub-9002_ses-1.anat_template_edge_0', 1.0) ('resting_preproc_sub-9002_ses-1.montage_mni_anat_1.resample_o', 1.0) ('resting_preproc_sub-9002_ses-1.montage_mni_anat_0.resample_o', 1.0) ('resting_preproc_sub-9002_ses-1.scan_params_0', 0.0) ('resting_preproc_sub-9002_ses-1.spatial_map_dataflow_for_DR_0.check_for_s3', 0.0) ('resting_preproc_sub-9002_ses-1.spatial_map_dataflow_1.check_for_s3', 0.0) ('resting_preproc_sub-9002_ses-1.roi_dataflow_0.check_for_s3', 0.0) ('resting_preproc_sub-9002_ses-1.roi_dataflow_for_sca_0.check_for_s3', 0.0) ('resting_preproc_sub-9002_ses-1.roi_dataflow_for_mult_reg_0.check_for_s3', 0.0) ('resting_preproc_sub-9002_ses-1.roi_dataflow_1.check_for_s3', 0.0) ('resting_preproc_sub-9002_ses-1.roi_dataflow_for_sca_1.check_for_s3', 0.0) ('resting_preproc_sub-9002_ses-1.roi_dataflow_for_mult_reg_1.check_for_s3', 0.0) ('resting_preproc_sub-9002_ses-1.anat_preproc_afni_0.anat_skullstrip_args', 0.0) ('resting_preproc_sub-9002_ses-1.check_for_s3_templateSpecificationFile', 0.0) ('resting_preproc_sub-9002_ses-1.check_for_s3_lateral_ventricles_mask', 0.0) ('resting_preproc_sub-9002_ses-1.resampled_template_skull_for_func_preproc', 0.0) ('resting_preproc_sub-9002_ses-1.resampled_template_symmetric_skull', 0.0) ('resting_preproc_sub-9002_ses-1.resampled_template_symmetric_brain', 0.0) ('resting_preproc_sub-9002_ses-1.resampled_template_skull_for_anat', 0.0) ('resting_preproc_sub-9002_ses-1.resampled_template_brain_for_anat', 0.0) |

FCP-INDI / cpac_run_logs