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ds003346-mriqc: "The 'in_file' trait of a _ReadSidecarJSONInputSpec instance must be a path like object or string representing an existing file" #75

Open jbwexler opened 11 months ago

jbwexler commented 11 months ago

For most subjects:

Traceback (most recent call last): File "/opt/conda/bin/mriqc", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.9/site-packages/mriqc/cli/run.py", line 168, in main mriqc_wf.run(**_plugin) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/workflows.py", line 628, in run execgraph = generate_expanded_graph(deepcopy(flatgraph)) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/utils.py", line 1188, in generate_e xpanded_graph return _remove_nonjoin_identity_nodes(graph_in) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/utils.py", line 847, in _remove_non join_identity_nodes _remove_identity_node(graph, node) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/utils.py", line 875, in _remove_ide ntity_node _propagate_root_output(graph, node, field, connections) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/utils.py", line 914, in propagate root_output destnode.set_input(inport, value) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 312, in set_input setattr(self.inputs, parameter, deepcopy(val)) File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate value = super(File, self).validate(objekt, name, value, return_pathlike=True) File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate self.error(objekt, name, str(value)) File "/opt/conda/lib/python3.9/site-packages/traits/base_trait_handler.py", line 74, in error raise TraitError( traits.trait_errors.TraitError: The 'in_file' trait of a ReadSidecarJSONInputSpec instance must be a pat hlike object or string representing an existing file, but a value of '/scratch1/03201/jbwexler/openneuro derivatives/derivatives/mriqc/ds003346-mriqc/sourcedata/raw/sub-011/dwi/sub-011_dwi.nii.gz' <class 'str'> was specified.