[BUG] FileNotFoundError: [Errno 2] No such file or directory

[oesteban]

Possibly a problem of nipype itself, but so far I've only seen it in fmriprep. Previously reported under #821, but unrelated to the original cause of that issue.

Node: fmriprep_wf.single_subject_MSC08_wf.func_preproc_ses_func10_task_memorywords_wf.bold_reg_wf.bbreg_wf.mri_coreg
Working directory: /scratch/users/oesteban/fmriprep-phase1/work/ds000224/fmriprep_wf/single_subject_MSC08_wf/func_preproc_ses_func10_task_memorywords_wf/bold_reg_wf/bbreg_wf/mri_coreg

Node inputs:

args = <undefined>
brute_force_limit = <undefined>
brute_force_samples = <undefined>
compress_report = auto
conform_reference = <undefined>
dof = 9
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'}
ftol = 0.0001
generate_report = True
ignore_exception = False
initial_rotation = <undefined>
initial_scale = <undefined>
initial_shear = <undefined>
initial_translation = <undefined>
linmintol = 0.01
max_iters = <undefined>
no_brute_force = <undefined>
no_coord_dithering = <undefined>
no_cras0 = <undefined>
no_intensity_dithering = <undefined>
no_smooth = <undefined>
num_threads = 8
out_lta_file = True
out_params_file = <undefined>
out_reg_file = <undefined>
out_report = report.svg
ref_fwhm = <undefined>
reference_file = <undefined>
reference_mask = <undefined>
saturation_threshold = <undefined>
sep = [4]
source_file = /scratch/users/oesteban/fmriprep-phase1/work/ds000224/fmriprep_wf/single_subject_MSC08_wf/func_preproc_ses_func10_task_memorywords_wf/nonlinear_sdc_wf/skullstrip_bold_wf/apply_mask/ants_susceptibility_Warped_masked.nii.gz
source_mask = <undefined>
source_oob = <undefined>
subject_id = sub-MSC08
subjects_dir = /oak/stanford/groups/russpold/data/openfmri/derivatives/ds000224/freesurfer
terminal_output = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 51, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 407, in run
    self._run_interface()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 515, in _run_interface
    old_cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory

and

Node: fmriprep_wf.single_subject_13_wf.func_preproc_task_dis_run_02_wf.bold_reg_wf.bbreg_wf.bbregister
Working directory: /scratch/users/oesteban/fmriprep-phase2/work/ds000212/fmriprep_wf/single_subject_13_wf/func_preproc_task_dis_run_02_wf/bold_reg_wf/bbreg_wf/bbregister

Node inputs:

args = <undefined>
compress_report = auto
contrast_type = t2
dof = 9
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects'}
epi_mask = <undefined>
fsldof = <undefined>
generate_report = True
ignore_exception = False
init = <undefined>
init_cost_file = <undefined>
init_reg_file = /scratch/users/oesteban/fmriprep-phase2/work/ds000212/fmriprep_wf/single_subject_13_wf/func_preproc_task_dis_run_02_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta
intermediate_file = <undefined>
out_fsl_file = <undefined>
out_lta_file = True
out_reg_file = <undefined>
out_report = report.svg
reg_frame = <undefined>
reg_middle_frame = <undefined>
registered_file = True
source_file = /scratch/users/oesteban/fmriprep-phase2/work/ds000212/fmriprep_wf/single_subject_13_wf/func_preproc_task_dis_run_02_wf/nonlinear_sdc_wf/skullstrip_bold_wf/apply_mask/ants_susceptibility_Warped_masked.nii.gz
spm_nifti = <undefined>
subject_id = sub-13
subjects_dir = /oak/stanford/groups/russpold/data/openfmri/derivatives/ds000212/freesurfer
terminal_output = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 51, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 407, in run
    self._run_interface()
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 515, in _run_interface
    old_cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory

[meng-du]

Hi, I'm getting this error too in a few different workflow (bold_mni_trans_wf/bold_to_mni_transform, bold_mni_trans_wf/merge, bold_reg_wf/bold_to_t1w_transform and a few components of bold_surf_wf). Is nipy/nipype #2325 supposed to be a fix?

Thank you!

[oesteban]

I'm testing it out, but to be sure it will require that I understand why this error is actually happening

[oesteban]

@metad are you using docker or singularity?

[meng-du]

@oesteban No I'm just using it with native python/pip

[oesteban]

That's great:

pip install niworkflows --upgrade

should work for you

[meng-du]

Awesome thank you so much!

[oesteban]

Please let us know if it resolved the problem :)

[meng-du]

Yes it's resolved!

[oesteban]

Fixed in 750724b