240125-00:41:37,902 nipype.workflow INFO: [Node] Setting-up "qsiprep_wf.single_subject_F1098_wf.dwi_preproc_wf.hmc_sdc_wf.eddy" in "/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy". 240125-00:41:37,906 nipype.workflow INFO: [Node] Executing "eddy" 240125-00:41:37,960 nipype.interface INFO: Re-orienting /scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/pre_eddy_b0_ref_wf/synthstrip_wf/mask_to_original_grid/topup_imain_corrected_avg_trans_mask_trans.nii.gz to LPS 240125-00:41:37,983 nipype.workflow INFO: [Node] Finished "b0_ref_mask_to_lps", elapsed time 0.081777s. 240125-00:41:37,990 nipype.workflow INFO: [Node] Finished "eddy", elapsed time 0.082986s. 240125-00:41:37,990 nipype.workflow WARNING: Storing result file without outputs 240125-00:41:37,991 nipype.workflow WARNING: [Node] Error on "qsiprep_wf.single_subject_F1098_wf.dwi_preproc_wf.hmc_sdc_wf.eddy" (/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy) 240125-00:41:38,153 nipype.workflow INFO: [Node] Finished "mask_brain", elapsed time 0.117641s. 240125-00:41:39,842 nipype.workflow ERROR: Node eddy failed to run on host 796d9e41d543. 240125-00:41:39,846 nipype.workflow ERROR: Saving crash info to /out/qsiprep/sub-F1098/log/20240125-002821_b7ec3b60-b48f-498d-9a16-6a4b80bf5607/crash-20240125-004139-root-eddy-6020a363-1f5e-4947-8579-770a58cde432.txt Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command raise NodeExecutionError(msg) nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node eddy. Cmdline: eddy_cuda --ol_nstd=4 --cnr_maps --estimate_move_by_susceptibility --field=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/topup/fieldmap_HZ --field_mat=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/topup_to_eddy_reg/topup_reg_image_flirt.mat --flm=quadratic --ff=10.0 --acqp=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/gather_inputs/eddy_acqp.txt --bvals=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.bval --bvecs=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.bvec --imain=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.nii.gz --index=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/gather_inputs/eddy_index.txt --mask=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/pre_eddy_b0_ref_wf/synthstrip_wf/mask_to_original_grid/topup_imain_corrected_avg_trans_mask_trans.nii.gz --interp=spline --data_is_shelled --resamp=jac --mporder=10 --niter=5 --nvoxhp=1000 --out=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected --repol --residuals --slspec=/data/code/slspec.txt --slm=linear Stdout: Stderr: eddy_cuda: error while loading shared libraries: libcublas.so.10: cannot open shared object file: No such file or directory Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs setattr(outputs, key, val) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate value = super(File, self).validate(objekt, name, value, return_pathlike=True) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate self.error(objekt, name, str(value)) File "/usr/local/miniconda/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error raise TraitError( traits.trait_errors.TraitError: The 'out_corrected' trait of an ExtendedEddyOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.nii.gz' was specified. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 400, in run outputs = self.aggregate_outputs(runtime) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs raise FileNotFoundError(msg) FileNotFoundError: No such file or directory '/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.nii.gz' for output 'out_corrected' of a ExtendedEddy interface QSIPrep failed: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command raise NodeExecutionError(msg) nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node eddy. Cmdline: eddy_cuda --ol_nstd=4 --cnr_maps --estimate_move_by_susceptibility --field=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/topup/fieldmap_HZ --field_mat=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/topup_to_eddy_reg/topup_reg_image_flirt.mat --flm=quadratic --ff=10.0 --acqp=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/gather_inputs/eddy_acqp.txt --bvals=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.bval --bvecs=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.bvec --imain=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.nii.gz --index=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/gather_inputs/eddy_index.txt --mask=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/pre_eddy_b0_ref_wf/synthstrip_wf/mask_to_original_grid/topup_imain_corrected_avg_trans_mask_trans.nii.gz --interp=spline --data_is_shelled --resamp=jac --mporder=10 --niter=5 --nvoxhp=1000 --out=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected --repol --residuals --slspec=/data/code/slspec.txt --slm=linear Stdout: Stderr: eddy_cuda: error while loading shared libraries: libcublas.so.10: cannot open shared object file: No such file or directory Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs setattr(outputs, key, val) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate value = super(File, self).validate(objekt, name, value, return_pathlike=True) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate self.error(objekt, name, str(value)) File "/usr/local/miniconda/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error raise TraitError( traits.trait_errors.TraitError: The 'out_corrected' trait of an ExtendedEddyOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.nii.gz' was specified. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 400, in run outputs = self.aggregate_outputs(runtime) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs raise FileNotFoundError(msg) FileNotFoundError: No such file or directory '/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.nii.gz' for output 'out_corrected' of a ExtendedEddy interface Traceback (most recent call last): File "/usr/local/miniconda/bin/qsiprep", line 8, in sys.exit(main()) File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/cli/run.py", line 677, in main qsiprep_wf.run(**plugin_settings) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 178, in run self._clean_queue(jobid, graph, result=result) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 256, in _clean_queue raise RuntimeError("".join(result["traceback"])) RuntimeError: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command raise NodeExecutionError(msg) nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node eddy. Cmdline: eddy_cuda --ol_nstd=4 --cnr_maps --estimate_move_by_susceptibility --field=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/topup/fieldmap_HZ --field_mat=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/topup_to_eddy_reg/topup_reg_image_flirt.mat --flm=quadratic --ff=10.0 --acqp=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/gather_inputs/eddy_acqp.txt --bvals=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.bval --bvecs=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.bvec --imain=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/pre_hmc_wf/rpe_concat/merge__merged.nii.gz --index=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/gather_inputs/eddy_index.txt --mask=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/pre_eddy_b0_ref_wf/synthstrip_wf/mask_to_original_grid/topup_imain_corrected_avg_trans_mask_trans.nii.gz --interp=spline --data_is_shelled --resamp=jac --mporder=10 --niter=5 --nvoxhp=1000 --out=/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected --repol --residuals --slspec=/data/code/slspec.txt --slm=linear Stdout: Stderr: eddy_cuda: error while loading shared libraries: libcublas.so.10: cannot open shared object file: No such file or directory Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs setattr(outputs, key, val) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate value = super(File, self).validate(objekt, name, value, return_pathlike=True) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate self.error(objekt, name, str(value)) File "/usr/local/miniconda/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error raise TraitError( traits.trait_errors.TraitError: The 'out_corrected' trait of an ExtendedEddyOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.nii.gz' was specified. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 400, in run outputs = self.aggregate_outputs(runtime) File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs raise FileNotFoundError(msg) FileNotFoundError: No such file or directory '/scratch/qsiprep_wf/single_subject_F1098_wf/dwi_preproc_wf/hmc_sdc_wf/eddy/eddy_corrected.nii.gz' for output 'out_corrected' of a ExtendedEddy interface 240125-00:43:57,895 nipype.workflow INFO: [Node] Finished "acpc_reg", elapsed time 582.441793s. qsiprep: Please report errors to https://github.com/pennbbl/qsiprep/issues