search

HBClab / SoftwareIssues

Issues when running primarily fmriprep/mriqc/xcpengine (primarily on argon)
0 stars 0 forks source link

CREST fmriprep: node and OS error #11

Open ariveradompenciel opened 4 years ago

ariveradompenciel commented 4 years ago

Script/Job File

#!/bin/bash

#$ -pe smp 16
#$ -q UI
#$ -m bea
#$ -M adriana-rivera-dompenciel@uiowa.edu
#$ -o /Shared/vosslabhpc/Projects/CREST/code/fmriprep/out/
#$ -e /Shared/vosslabhpc/Projects/CREST/code/fmriprep/err/
OMP_NUM_THREADS=10
singularity run -H ${HOME}/singularity_home -B /Shared/vosslabhpc:/mnt \
/Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg \
/mnt/Projects/CREST/ /mnt/Projects/CREST/derivatives \
participant --participant_label OPTIMA4062 \
-w /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep \
--write-graph --mem_mb 35000 --omp-nthreads 10 --nthreads 16 --use-aroma \
--output-space template \
--template MNI152NLin2009cAsym \
--fs-license-file /mnt/UniversalSoftware/freesurfer_license.txt

Email Message

Job 9534820 (sub-OPTIMA4062.job) Complete
User             = ariveradompenciel
Queue            = UI@argon-itf-cf45-25.hpc
Host             = argon-itf-cf45-25.hpc
Start Time       = 04/08/2020 18:16:26
End Time         = 04/08/2020 18:33:14
User Time        = 00:00:52
System Time      = 00:00:02
Wallclock Time   = 00:16:48
CPU              = 01:32:04
Max vmem         = 5.001G
Exit Status      = 1

Output File

200408-18:16:31,866 nipype.workflow IMPORTANT:

    Running fMRIPREP version 1.2.1:
      * BIDS dataset path: /mnt/Projects/CREST.
      * Participant list: ['OPTIMA4062'].
      * Run identifier: 20200408-181631_16e6b21c-ad14-4682-9c2d-beaf4eec0210.

200408-18:16:31,866 nipype.workflow WARNING:
     Option --debug is deprecated and has no effect
200408-18:16:39,250 nipype.workflow IMPORTANT:
     Creating bold processing workflow for "/mnt/Projects/CREST/sub-OPTIMA4062/func/sub-OPTIMA4062_task-rest_bold.nii.gz" (0.03 GB / 180 TRs). Memory resampled/largemem=0.13/0.18 GB.
200408-18:16:39,284 nipype.workflow IMPORTANT:
     No single-band-reference found for sub-OPTIMA4062_task-rest_bold.nii.gz
200408-18:16:39,721 nipype.workflow WARNING:
     SDC: no fieldmaps found or they were ignored (/mnt/Projects/CREST/sub-OPTIMA4062/func/sub-OPTIMA4062_task-rest_bold.nii.gz).
200408-18:16:44,845 nipype.workflow IMPORTANT:
     Works derived from this fMRIPrep execution should include the following boilerplate:

Results included in this manuscript come from preprocessing
performed using *fMRIPprep* 1.2.1
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.1.4
(@nipype1; @nipype2; RRID:SCR_002502).

Anatomical data preprocessing

: The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
using `N4BiasFieldCorrection` [@n4, ANTs 2.2.0],
and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped using `antsBrainExtraction.sh`
(ANTs 2.2.0), using OASIS as target template.
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
Spatial normalization to the ICBM 152 Nonlinear Asymmetrical
template version 2009c [@mni, RRID:SCR_008796] was performed
through nonlinear registration with `antsRegistration`
[ANTs 2.2.0, RRID:SCR_004757, @ants], using
brain-extracted versions of both T1w volume and template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823,
@fsl_fast].

Functional data preprocessing

: For each of the 1 BOLD runs found per subject (across all
tasks and sessions), the following preprocessing was performed.
First, a reference volume and its skull-stripped version were generated
using a custom methodology of *fMRIPrep*.
The BOLD reference was then co-registered to the T1w reference using
`bbregister` (FreeSurfer) which implements boundary-based registration [@bbr].
Co-registration was configured with nine degrees of freedom to account
for distortions remaining in the BOLD reference.
Head-motion parameters with respect to the BOLD reference
(transformation matrices, and six corresponding rotation and translation
parameters) are estimated before any spatiotemporal filtering using
`mcflirt` [FSL 5.0.9, @mcflirt].
The BOLD time-series (including slice-timing correction when applied)
were resampled onto their original, native space by applying
a single, composite transform to correct for head-motion and
susceptibility distortions.
These resampled BOLD time-series will be referred to as *preprocessed
BOLD in original space*, or just *preprocessed BOLD*.
First, a reference volume and its skull-stripped version were generated
using a custom methodology of *fMRIPrep*.
Automatic removal of motion artifacts using independent component analysis
[ICA-AROMA, @aroma] was performed on the *preprocessed BOLD on MNI space*
time-series after removal of non-steady state volumes and spatial smoothing
with an isotropic, Gaussian kernel of 6mm FWHM (full-width half-maximum).
Corresponding "non-aggresively" denoised runs were produced after such
smoothing.
Additionally, the "aggressive" noise-regressors were collected and placed
in the corresponding confounds file.
The BOLD time-series were resampled to MNI152NLin2009cAsym standard space,
generating a *preprocessed BOLD run in MNI152NLin2009cAsym space*.
First, a reference volume and its skull-stripped version were generated
using a custom methodology of *fMRIPrep*.
Several confounding time-series were calculated based on the
*preprocessed BOLD*: framewise displacement (FD), DVARS and
three region-wise global signals.
FD and DVARS are calculated for each functional run, both using their
implementations in *Nipype* [following the definitions by @power_fd_dvars].
The three global signals are extracted within the CSF, the WM, and
the whole-brain masks.
Additionally, a set of physiological regressors were extracted to
allow for component-based noise correction [*CompCor*, @compcor].
Principal components are estimated after high-pass filtering the
*preprocessed BOLD* time-series (using a discrete cosine filter with
128s cut-off) for the two *CompCor* variants: temporal (tCompCor)
and anatomical (aCompCor).
Six tCompCor components are then calculated from the top 5% variable
voxels within a mask covering the subcortical regions.
This subcortical mask is obtained by heavily eroding the brain mask,
which ensures it does not include cortical GM regions.
For aCompCor, six components are calculated within the intersection of
the aforementioned mask and the union of CSF and WM masks calculated
in T1w space, after their projection to the native space of each
functional run (using the inverse BOLD-to-T1w transformation).
The head-motion estimates calculated in the correction step were also
placed within the corresponding confounds file.
All resamplings can be performed with *a single interpolation
step* by composing all the pertinent transformations (i.e. head-motion
transform matrices, susceptibility distortion correction when available,
and co-registrations to anatomical and template spaces).
Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs),
configured with Lanczos interpolation to minimize the smoothing
effects of other kernels [@lanczos].
Non-gridded (surface) resamplings were performed using `mri_vol2surf`
(FreeSurfer).

Many internal operations of *fMRIPrep* use
*Nilearn* 0.4.2 [@nilearn, RRID:SCR_001362],
mostly within the functional processing workflow.
For more details of the pipeline, see [the section corresponding
to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation").

### References

200408-18:17:00,293 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_reference_wf.validate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_reference_wf/validate".
200408-18:17:00,329 nipype.workflow INFO:
     [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage")
200408-18:17:00,455 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.bidssrc" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/bidssrc".
200408-18:17:00,889 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_reference_wf.validate".
200408-18:17:00,898 nipype.workflow INFO:
     [Node] Running "bidssrc" ("fmriprep.interfaces.bids.BIDSDataGrabber")
200408-18:17:00,900 nipype.interface WARNING:
     No 't2w' images found for sub-<undefined>
200408-18:17:00,900 nipype.interface WARNING:
     No 'flair' images found for sub-<undefined>
200408-18:17:00,900 nipype.interface WARNING:
     No 'sbref' images found for sub-<undefined>
200408-18:17:00,900 nipype.interface WARNING:
     No 'roi' images found for sub-<undefined>
200408-18:17:00,922 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.bidssrc".
200408-18:17:03,381 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_split" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_split".
200408-18:17:03,398 nipype.workflow INFO:
     [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command:
fslsplit /mnt/Projects/CREST/sub-OPTIMA4062/func/sub-OPTIMA4062_task-rest_bold.nii.gz -t
200408-18:17:04,397 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref".
200408-18:17:04,618 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions".
200408-18:17:04,634 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage")
200408-18:17:04,639 nipype.workflow INFO:
     [Node] Running "t1_template_dimensions" ("fmriprep.interfaces.images.TemplateDimensions")
200408-18:17:05,35 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions".
200408-18:17:06,117 nipype.interface INFO:
     stderr 2020-04-08T18:17:06.117486:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit]
200408-18:17:06,118 nipype.interface INFO:
     stderr 2020-04-08T18:17:06.117486:++ Authored by: RW Cox
200408-18:17:06,123 nipype.interface INFO:
     stderr 2020-04-08T18:17:06.123168:++ Coarse del was 10, replaced with 3
200408-18:17:08,696 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/anat_preproc_wf/anat_derivatives_wf/t1_name".
200408-18:17:08,712 nipype.workflow INFO:
     [Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function")
200408-18:17:08,730 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.anat_derivatives_wf.t1_name".
200408-18:17:09,708 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/anat_preproc_wf/anat_template_wf/t1_conform".
200408-18:17:09,736 nipype.workflow INFO:
     [Node] Setting-up "_t1_conform0" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0".
200408-18:17:09,752 nipype.workflow INFO:
     [Node] Running "_t1_conform0" ("fmriprep.interfaces.images.Conform")
200408-18:17:11,35 nipype.workflow INFO:
     [Node] Finished "_t1_conform0".
200408-18:17:11,49 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.anat_template_wf.t1_conform".
200408-18:17:13,392 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip".
200408-18:17:13,424 nipype.workflow INFO:
     [Node] Running "t1_skull_strip" ("nipype.interfaces.ants.segmentation.BrainExtraction"), a CommandLine Interface with command:
antsBrainExtraction.sh -a /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-OPTIMA4062_T1w_ras.nii.gz -m /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz -e /niworkflows_data/ants_oasis_template_ras/T_template0.nii.gz -d 3 -f /niworkflows_data/ants_oasis_template_ras/T_template0_BrainCerebellumRegistrationMask.nii.gz -s nii.gz -k 1 -o highres001_ -q 1 -u 1
200408-18:17:14,357 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/anat_preproc_wf/surface_recon_wf/recon_config".
200408-18:17:14,392 nipype.workflow INFO:
     [Node] Running "recon_config" ("fmriprep.interfaces.freesurfer.FSDetectInputs")
200408-18:17:14,427 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.surface_recon_wf.recon_config".
200408-18:17:19,377 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_split".
200408-18:17:22,225 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref".
200408-18:17:22,241 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference")
200408-18:17:22,260 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.ica_aroma_wf.bold_mni_trans_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/ica_aroma_wf/bold_mni_trans_wf/gen_ref".
200408-18:17:22,306 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference")
200408-18:17:22,777 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.ica_aroma_wf.bold_mni_trans_wf.gen_ref".
200408-18:17:22,779 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref".
200408-18:17:24,128 nipype.interface INFO:
     stderr 2020-04-08T18:17:24.128223:++ Max displacement in automask = 0.41 (mm) at sub-brick 19
200408-18:17:24,128 nipype.interface INFO:
     stderr 2020-04-08T18:17:24.128223:++ Max delta displ  in automask = 0.27 (mm) at sub-brick 19
200408-18:17:25,370 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref".
200408-18:17:28,475 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref".
200408-18:17:28,517 nipype.workflow INFO:
     [Node] Running "validate_ref" ("fmriprep.interfaces.images.ValidateImage")
200408-18:17:28,561 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref".
200408-18:17:31,626 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt".
200408-18:17:31,646 nipype.workflow INFO:
     [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /mnt/Projects/CREST/sub-OPTIMA4062/func/sub-OPTIMA4062_task-rest_bold.nii.gz -out /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt/sub-OPTIMA4062_task-rest_bold_mcf.nii.gz -reffile /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/ref_image.nii.gz -mats -plots
200408-18:18:15,124 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt".
200408-18:18:18,453 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_hmc_wf/normalize_motion".
200408-18:18:18,468 nipype.workflow INFO:
     [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams")
200408-18:18:18,497 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion".
200408-18:18:20,313 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_confounds_wf/fdisp".
200408-18:18:20,541 nipype.workflow INFO:
     [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement")
200408-18:18:20,578 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp".
200408-18:32:17,346 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip".
200408-18:32:18,758 nipype.workflow WARNING:
     [Node] Error on "fmriprep_wf.single_subject_OPTIMA4062_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_preproc" (/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_preproc)
200408-18:32:18,770 nipype.workflow ERROR:
     Node ds_t1_preproc failed to run on host argon-itf-cf45-25.hpc.
200408-18:32:20,601 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_OPTIMA4062_wf/func_preproc_task_rest_wf/bold_hmc_wf/fsl2itk".
200408-18:32:20,626 nipype.workflow INFO:
     [Node] Running "fsl2itk" ("fmriprep.interfaces.itk.MCFLIRT2ITK")
200408-18:33:14,316 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_OPTIMA4062_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk".
Sentry is attempting to send 1 pending error messages
Waiting up to 10 seconds
Press Ctrl-C to quit

Error (stderr file)

/usr/local/miniconda/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
  warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata.
  Falling back to 'CITATION'
/usr/local/miniconda/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
  warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:116: UserWarning: 'dataset_description.json' file is missing from project root. You may want to set the root path to a valid BIDS project.
  warnings.warn("'dataset_description.json' file is missing from "
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 308, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/bids.py", line 252, in _run_interface
    os.makedirs(out_path, exist_ok=True)
  File "/usr/local/miniconda/lib/python3.6/os.py", line 210, in makedirs
    makedirs(head, mode, exist_ok)
  File "/usr/local/miniconda/lib/python3.6/os.py", line 210, in makedirs
    makedirs(head, mode, exist_ok)
  File "/usr/local/miniconda/lib/python3.6/os.py", line 210, in makedirs
    makedirs(head, mode, exist_ok)
  [Previous line repeated 1 more times]
  File "/usr/local/miniconda/lib/python3.6/os.py", line 220, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/mnt/Projects'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 791, in makedirs
    os.makedirs(path)
  File "/usr/local/miniconda/lib/python3.6/os.py", line 210, in makedirs
    makedirs(head, mode, exist_ok)
  File "/usr/local/miniconda/lib/python3.6/os.py", line 210, in makedirs
    makedirs(head, mode, exist_ok)
  File "/usr/local/miniconda/lib/python3.6/os.py", line 210, in makedirs
    makedirs(head, mode, exist_ok)
  [Previous line repeated 2 more times]
  File "/usr/local/miniconda/lib/python3.6/os.py", line 220, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/mnt/Projects'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda/bin/fmriprep", line 11, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 342, in main
    fmriprep_wf.run(**plugin_settings)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py", line 595, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py", line 184, in run
    self._send_procs_to_workers(updatehash=updatehash, graph=graph)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 316, in _send_procs_to_workers
    'traceback': traceback
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py", line 225, in _clean_queue
    crashfile = self._report_crash(self.procs[jobid], result=result)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py", line 209, in _report_crash
    return report_crash(node, traceback=tb)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/tools.py", line 49, in report_crash
    makedirs(crashdir, exist_ok=True)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/utils/filemanip.py", line 795, in makedirs
    raise OSError('Could not create directory %s' % path)
OSError: Could not create directory /mnt/Projects/CREST/derivatives/fmriprep/sub-OPTIMA4062/log/20200408-181631_16e6b21c-ad14-4682-9c2d-beaf4eec0210
jdkent commented 4 years ago

This appears to be a symptom of the permission errors you got yesterday, here's the relevant bit: PermissionError: [Errno 13] Permission denied: '/mnt/Projects', so the permissions issue needs to be fixed to move this forward.