Hi there,
I just upgraded to qunex container version 0.100.0, and whenever I run the container I get a python error of KeyboardInterrupt.
I use run_turnkey, after map_raw_data was done so steps start with import_dicom.
Call:
qunex_container run_turnkey
--rawdatainput="${RAW_DATA}"
--paramfile="${INPUT_BATCH_FILE}"
--mappingfile="${INPUT_MAPPING_FILE}"
--workingdir="${WORK_DIR}"
--projectname="${STUDY_NAME}"
--path="${WORK_DIR}/${STUDY_NAME}"
--sessions="${SESSIONS}"
--sessionsfolder="${STUDY_FOLDER}/sessions"
--turnkeytype="${RUNTURNKEY_TYPE}"
--container="${QUNEX_CONTAINER}"
--turnkeysteps="${RUNTURNKEY_STEPS}"
--parelements=3
--dockeropt="-v ${BIND_FOLDER}:${BIND_FOLDER}"
where
export QUNEX_CONTAINER="gitlab.qunex.yale.edu:5002/qunex/qunexcontainer:0.100.0"
export RUNTURNKEY_STEPS="import_dicom,create_session_info,setup_hcp,create_batch,hcp_pre_freesurfer,hcp_freesurfer,hcp_post_freesurfer,hcp_fmri_volume,hcp_fmri_surface"
Logs:
Binary / Executable Locations and Versions
----------------------------------------------
HCPpipelines TAG : v4.8.0-rc
HCPpipelines commit : 62c6fff3f1e258746c5cc18890eef81a5cbb8696
HCP ASL commit : 9e8b06c56b685c9a07cc91a839161704aede1d0d
FSL Binary :
FSL Version : Binary not found!
FreeSurfer Binary :
FreeSurfer Version : Binary not found!
AFNI Binary :
AFNI Version : Binary not found!
ANTs Binary :
ANTs Version : Binary not found!
dcm2niix Binary :
dcm2niix Version : Binary not found!
FIX Binary :
FIX Version : Binary not found!
Octave Binary :
Octave Version : Binary not found!
R Binary :
R Version : Binary not found!
python binary :
python : Binary not found!
PALM Binary : /opt/palm/palm-o/palm.m
PALM Version : Mar/2024 (github)
wb_command Binary :
wb_command Version : Binary not found!
Full Environment Paths
----------------------------------------------
PATH : /opt/env/qunex/bin:/opt/miniconda/bin:/opt/fsl/fsl-6.0.7.11/condabin:/usr/local/cuda/bin:/opt/HCP/HCPpipelines/global/matlab:/opt/fsl/fix:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended:/opt/qunex/bash/qx_utilities:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense:/opt/qunex/bash/qx_utilities/diffusion_tractography/scripts:/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts:/opt/HCP/HCPpipelines/global/scripts:/opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts:/opt/HCP/HCPpipelines/tfMRI/scripts:/opt/HCP/HCPpipelines/fMRIVolume/scripts:/opt/HCP/HCPpipelines/fMRISurface/scripts:/opt/HCP/HCPpipelines/PostFreeSurfer/scripts:/opt/HCP/HCPpipelines/FreeSurfer/scripts:/opt/HCP/HCPpipelines/PreFreeSurfer/scripts:/opt/HCP/HCPpipelines/global/config:/opt/HCP/HCPpipelines/global/binaries:/opt/HCP/HCPpipelines/global/templates:/opt/gradunwarp/gradunwarp/gradunwarp/core:/opt/workbench/workbench/bin_linux64:/opt/HCP/HCPpipelines:/opt/HCP/HCPpipelines/MSMConfig:/opt/qunex/python/qx_utilities/templates:/opt/qunex/qx_library/data:/opt/qunex/qx_library/data/atlases/hcp:/opt/R/R:/opt/matlab/bin:/opt/octave/octave/bin:/opt/dcm2niix/dcm2niix:/opt/dcm2niix/dcm2niix/bin:/opt/ANTs/ANTs/bin:/opt/AFNI/AFNI:/opt/palm/palm-o:/opt/workbench/workbench/bin_linux64:/opt/freesurfer/FreeSurferScheduler:/opt/fsl/fsl/share/fsl/bin:/opt/freesurfer/freesurfer/bin:/opt/freesurfer/freesurfer/fsfast/bin:/opt/freesurfer/freesurfer/tktools:/opt/fsl/fsl/bin:/opt/fsl/fsl/share/fsl/bin:/opt/freesurfer/freesurfer/mni/bin:/opt/freesurfer/freesurfer:/opt/freesurfer/freesurfer/bin:/opt/freesurfer/freesurfer/mni/bin:/opt/qunex/lib:/opt/qunex/bin:/opt/bin:/opt/lib/bin:/opt/lib/lib:/opt/olib:/opt/qunex/python/qx_utilities:/opt:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/bin:/opt/fsl/fsl/bin:/opt/fsl/fsl/etc/matlab:/opt/fsl/fsl/lib
MATLABPATH : /opt/qunex/matlab/qx_mice:/opt/qunex/matlab/qx_utilities/general:/opt/qunex/matlab/qx_mri/stats:/opt/qunex/matlab/qx_mri/img:/opt/qunex/matlab/qx_mri/general:/opt/qunex/matlab/qx_mri/fc:/opt/HCP/HCPpipelines/global/matlab:/opt/HCP/HCPpipelines/global/matlab/cifti-matlab:/opt/HCP/HCPpipelines/global/matlab/icaDim:/opt/HCP/HCPpipelines/global/matlab/nets_spectra:/opt/HCP/HCPpipelines/global/matlab:/opt/fsl/fix:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/matlablib/cifti-matlab.qx:/opt/palm/palm-o:/opt/workbench/workbench/bin_linux64:/opt/fsl/fsl:/opt/fsl/fsl/bin:/opt/fsl/fsl/etc/matlab:
ERROR: The following binaries / executables are not found: fsl freesurfer afni ants dcm2niix fix octave R python wb_command
---------------------------------------------------------------------
---> Executing specific QuNex turkey workflow steps: import_dicom create_session_info setup_hcp create_batch hcp_pre_freesurfer hcp_freesurfer hcp_post_freesurfer hcp_fmri_volume hcp_fmri_surface
---------------------------------------------------------------------
---> RUNNING run_turnkey step ~~~ import_dicom
-- Executed call:
/opt/qunex/bin/qunex.sh import_dicom --sessionsfolder='/home/docker/volumes/hcppipelines/asaf_decoy_mouse/decoy/sessions' --sessions='035' --masterinbox='none' --archive='delete' --check='any' --unzip='yes' --add_image_type='' --add_json_info='' --gzip='folder' --overwrite='no'
........................ Running QuNex v0.100.0 [QX IO] ........................
OpenBLAS blas_thread_init: pthread_create failed for thread 1 of 40: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
...
OpenBLAS blas_thread_init: pthread_create failed for thread 39 of 40: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
Traceback (most recent call last):
File "/opt/qunex/python/qx_utilities/gmri", line 20, in <module>
from general import commands as gcom
File "/opt/qunex/python/qx_utilities/general/commands.py", line 15, in <module>
from general import dicom, bids, fourdfp, dicomdeid, fidl, qximg, img, nifti, palm, scheduler, utilities, meltmovfidl, commands_support, bruker, extensions
File "/opt/qunex/python/qx_utilities/general/dicom.py", line 47, in <module>
import general.nifti as gn
File "/opt/qunex/python/qx_utilities/general/nifti.py", line 26, in <module>
import numpy as np
File "/opt/env/qunex/lib/python3.12/site-packages/numpy/__init__.py", line 130, in <module>
from numpy.__config__ import show as show_config
File "/opt/env/qunex/lib/python3.12/site-packages/numpy/__config__.py", line 4, in <module>
from numpy.core._multiarray_umath import (
File "/opt/env/qunex/lib/python3.12/site-packages/numpy/core/__init__.py", line 24, in <module>
from . import multiarray
File "/opt/env/qunex/lib/python3.12/site-packages/numpy/core/multiarray.py", line 10, in <module>
from . import overrides
File "/opt/env/qunex/lib/python3.12/site-packages/numpy/core/overrides.py", line 8, in <module>
from numpy.core._multiarray_umath import (
File "<frozen importlib._bootstrap>", line 463, in _lock_unlock_module
KeyboardInterrupt
Thank you in advance for your help,
Asaf
