$> testkraken --help
Usage: testkraken [OPTIONS] PATH
This script runs the workflow in PATH.
but when I run with relative path it kabooms
```shell
(git)lena:~/.tmp/dl-kraken-yqaBPWM/testkraken[master]git
$> sudo rm -rf workflows4regtests/afni_dc2019/3dcopy_datalad/data/ ; testkraken workflows4regtests/afni_dc2019/3dcopy_datalad/
Installing test data
[INFO ] Scanning for unlocked files (this may take some time)
[INFO ] Remote origin not usable by git-annex; setting annex-ignore
running testkraken for workflows4regtests/afni_dc2019/3dcopy_datalad/; working directory - None
+ building 1 Docker images
++ building image: {'pkg_manager': 'apt', 'instructions': (('base', 'debian:stretch'), ('afni', {'version': 'latest'}))}
Sending build context to Docker daemon 6.144kB
Step 1/9 : FROM debian:stretch
---> 62ace29a8c8f
Step 2/9 : USER root
---> Using cache
---> 0a0242cabb6b
Step 3/9 : ARG DEBIAN_FRONTEND="noninteractive"
---> Using cache
---> 9b5957f75547
Step 4/9 : ENV LANG="en_US.UTF-8" LC_ALL="en_US.UTF-8" ND_ENTRYPOINT="/neurodocker/startup.sh"
---> Using cache
---> ee7c9c814662
Step 5/9 : RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" && apt-get update -qq && apt-get install -y -q --no-install-recommends apt-utils bzip2 ca-certificates curl locales unzip && apt-get clean && rm -rf /var/lib/apt/lists/* && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && dpkg-reconfigure --frontend=noninteractive locales && update-locale LANG="en_US.UTF-8" && chmod 777 /opt && chmod a+s /opt && mkdir -p /neurodocker && if [ ! -f "$ND_ENTRYPOINT" ]; then echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" && echo 'set -e' >> "$ND_ENTRYPOINT" && echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" && echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; fi && chmod -R 777 /neurodocker && chmod a+s /neurodocker
---> Using cache
---> 2ffd82e60498
Step 6/9 : ENTRYPOINT ["/neurodocker/startup.sh"]
---> Using cache
---> fe1ff4b56fc6
Step 7/9 : ENV PATH="/opt/afni-latest:$PATH" AFNI_PLUGINPATH="/opt/afni-latest"
---> Using cache
---> d65fc11a2624
Step 8/9 : RUN apt-get update -qq && apt-get install -y -q --no-install-recommends ed gsl-bin libglib2.0-0 libglu1-mesa-dev libglw1-mesa libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb && apt-get clean && rm -rf /var/lib/apt/lists/* && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb && dpkg -i /tmp/toinstall.deb && rm /tmp/toinstall.deb && curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb && dpkg -i /tmp/toinstall.deb && rm /tmp/toinstall.deb && apt-get install -f && apt-get clean && rm -rf /var/lib/apt/lists/* && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" && if [ -n "$gsl2_path" ]; then ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; fi && ldconfig && echo "Downloading AFNI ..." && mkdir -p /opt/afni-latest && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz | tar -xz -C /opt/afni-latest --strip-components 1
---> Using cache
---> b6b2afe5a112
Step 9/9 : RUN echo '{ \n "pkg_manager": "apt", \n "instructions": [ \n [ \n "base", \n "debian:stretch" \n ], \n [ \n "afni", \n { \n "version": "latest" \n } \n ] \n ] \n}' > /neurodocker/neurodocker_specs.json
---> Using cache
---> 3e626823d1a5
Successfully built 3e626823d1a5
Successfully tagged repronim/testkraken:a1f5db7b4e67ffa4aaba1de3db1bba4f65784325
running pydra workflow for workflows4regtests/afni_dc2019/3dcopy_datalad in working directory - /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw
Task exception was never retrieved
future: exception=RuntimeError('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load\n stat_result = os.stat(filename)\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_headers.py", line 38, in \n test_afni_scan_header(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_headers.py", line 11, in test_afni_scan_header\n image_ref = nib.load(str(file_ref))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load\n raise FileNotFoundError(f"No such file or no access: \'{filename}\'")\nFileNotFoundError: No such file or no access: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_84af85f5e1443291d154a97a613e9d3a97ad72cd5eff7bbf4f7a21a1bf749f18/_error.pklz')>
concurrent.futures.process._RemoteTraceback:
"""
RuntimeError: Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: 'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_headers.py", line 38, in
test_afni_scan_header(**vars(args))
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_headers.py", line 11, in test_afni_scan_header
image_ref = nib.load(str(file_ref))
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load
raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: 'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.9/concurrent/futures/process.py", line 243, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/helpers.py", line 789, in load_and_run
raise type(excinfo)(
RuntimeError: ('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load\n stat_result = os.stat(filename)\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_headers.py", line 38, in \n test_afni_scan_header(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_headers.py", line 11, in test_afni_scan_header\n image_ref = nib.load(str(file_ref))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load\n raise FileNotFoundError(f"No such file or no access: \'{filename}\'")\nFileNotFoundError: No such file or no access: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_84af85f5e1443291d154a97a613e9d3a97ad72cd5eff7bbf4f7a21a1bf749f18/_error.pklz')
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/workers.py", line 166, in exec_as_coro
res = await self.loop.run_in_executor(
RuntimeError: ('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load\n stat_result = os.stat(filename)\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_headers.py", line 38, in \n test_afni_scan_header(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_headers.py", line 11, in test_afni_scan_header\n image_ref = nib.load(str(file_ref))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load\n raise FileNotFoundError(f"No such file or no access: \'{filename}\'")\nFileNotFoundError: No such file or no access: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_84af85f5e1443291d154a97a613e9d3a97ad72cd5eff7bbf4f7a21a1bf749f18/_error.pklz')
Task exception was never retrieved
future: exception=RuntimeError('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load\n stat_result = os.stat(filename)\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data_diff_fake.py", line 44, in \n test_afni_scan_data_diff_fake(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data_diff_fake.py", line 14, in test_afni_scan_data_diff_fake\n image_ref = nib.load(str(file_ref))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load\n raise FileNotFoundError(f"No such file or no access: \'{filename}\'")\nFileNotFoundError: No such file or no access: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_194ec5f2a558f68c8d9a1709c2aea322fac683efa6533484796a47e32fe43463/_error.pklz')>
concurrent.futures.process._RemoteTraceback:
"""
RuntimeError: Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: 'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data_diff_fake.py", line 44, in
test_afni_scan_data_diff_fake(**vars(args))
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data_diff_fake.py", line 14, in test_afni_scan_data_diff_fake
image_ref = nib.load(str(file_ref))
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load
raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: 'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.9/concurrent/futures/process.py", line 243, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/helpers.py", line 789, in load_and_run
raise type(excinfo)(
RuntimeError: ('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load\n stat_result = os.stat(filename)\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data_diff_fake.py", line 44, in \n test_afni_scan_data_diff_fake(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data_diff_fake.py", line 14, in test_afni_scan_data_diff_fake\n image_ref = nib.load(str(file_ref))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load\n raise FileNotFoundError(f"No such file or no access: \'{filename}\'")\nFileNotFoundError: No such file or no access: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_194ec5f2a558f68c8d9a1709c2aea322fac683efa6533484796a47e32fe43463/_error.pklz')
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/workers.py", line 166, in exec_as_coro
res = await self.loop.run_in_executor(
RuntimeError: ('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load\n stat_result = os.stat(filename)\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data_diff_fake.py", line 44, in \n test_afni_scan_data_diff_fake(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data_diff_fake.py", line 14, in test_afni_scan_data_diff_fake\n image_ref = nib.load(str(file_ref))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load\n raise FileNotFoundError(f"No such file or no access: \'{filename}\'")\nFileNotFoundError: No such file or no access: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_194ec5f2a558f68c8d9a1709c2aea322fac683efa6533484796a47e32fe43463/_error.pklz')
Task exception was never retrieved
future: exception=RuntimeError('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_obj_eq.py", line 59, in \n test_obj_eq(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_obj_eq.py", line 21, in test_obj_eq\n with open(file_ref) as f:\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_3e2ccaa54b93aad5dda727cebbe49675846166eabeacbfbc540a645678ff8275/_error.pklz')>
concurrent.futures.process._RemoteTraceback:
"""
RuntimeError: Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_obj_eq.py", line 59, in
test_obj_eq(**vars(args))
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_obj_eq.py", line 21, in test_obj_eq
with open(file_ref) as f:
FileNotFoundError: [Errno 2] No such file or directory: 'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.9/concurrent/futures/process.py", line 243, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/helpers.py", line 789, in load_and_run
raise type(excinfo)(
RuntimeError: ('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_obj_eq.py", line 59, in \n test_obj_eq(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_obj_eq.py", line 21, in test_obj_eq\n with open(file_ref) as f:\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_3e2ccaa54b93aad5dda727cebbe49675846166eabeacbfbc540a645678ff8275/_error.pklz')
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/workers.py", line 166, in exec_as_coro
res = await self.loop.run_in_executor(
RuntimeError: ('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_obj_eq.py", line 59, in \n test_obj_eq(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_obj_eq.py", line 21, in test_obj_eq\n with open(file_ref) as f:\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_3e2ccaa54b93aad5dda727cebbe49675846166eabeacbfbc540a645678ff8275/_error.pklz')
Task exception was never retrieved
future: exception=RuntimeError('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load\n stat_result = os.stat(filename)\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data.py", line 42, in \n test_afni_scan_data(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data.py", line 14, in test_afni_scan_data\n image_ref = nib.load(str(file_ref))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load\n raise FileNotFoundError(f"No such file or no access: \'{filename}\'")\nFileNotFoundError: No such file or no access: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_f8969643f88f065e4ddc72ed042f6553b82fb03d240bcdda3ee7a724f79826a2/_error.pklz')>
concurrent.futures.process._RemoteTraceback:
"""
RuntimeError: Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: 'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data.py", line 42, in
test_afni_scan_data(**vars(args))
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data.py", line 14, in test_afni_scan_data
image_ref = nib.load(str(file_ref))
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load
raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: 'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.9/concurrent/futures/process.py", line 243, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/helpers.py", line 789, in load_and_run
raise type(excinfo)(
RuntimeError: ('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load\n stat_result = os.stat(filename)\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data.py", line 42, in \n test_afni_scan_data(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data.py", line 14, in test_afni_scan_data\n image_ref = nib.load(str(file_ref))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load\n raise FileNotFoundError(f"No such file or no access: \'{filename}\'")\nFileNotFoundError: No such file or no access: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_f8969643f88f065e4ddc72ed042f6553b82fb03d240bcdda3ee7a724f79826a2/_error.pklz')
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/workers.py", line 166, in exec_as_coro
res = await self.loop.run_in_executor(
RuntimeError: ('Traceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load\n stat_result = os.stat(filename)\nFileNotFoundError: [Errno 2] No such file or directory: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data.py", line 42, in \n test_afni_scan_data(**vars(args))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/testing_functions/test_afni_scan_data.py", line 14, in test_afni_scan_data\n image_ref = nib.load(str(file_ref))\n File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load\n raise FileNotFoundError(f"No such file or no access: \'{filename}\'")\nFileNotFoundError: No such file or no access: \'workflows4regtests/afni_dc2019/3dcopy_datalad/data_ref/copied.nii.gz\'\n', ' full crash report is here: /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw/ShellCommandTask_f8969643f88f065e4ddc72ed042f6553b82fb03d240bcdda3ee7a724f79826a2/_error.pklz')
Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/core.py", line 1088, in _collect_outputs
val_out = val.get_value(self)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/specs.py", line 785, in get_value
raise ValueError("Error from get_value")
ValueError: Error from get_value
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/bin/testkraken", line 11, in
load_entry_point('testkraken', 'console_scripts', 'testkraken')()
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/cli.py", line 24, in main
wf.run()
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/workflowregtest.py", line 117, in run
self._run_workflow_in_matrix_of_envs()
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/workflowregtest.py", line 160, in _run_workflow_in_matrix_of_envs
self._run_pydra(image=image, soft_ver_str=name)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/testkraken/workflowregtest.py", line 374, in _run_pydra
sub(wf)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/submitter.py", line 56, in __call__
self.loop.run_until_complete(self.submit_workflow(runnable, rerun=rerun))
File "/usr/lib/python3.9/asyncio/base_events.py", line 642, in run_until_complete
return future.result()
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/submitter.py", line 71, in submit_workflow
await workflow._run(self, rerun=rerun)
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/core.py", line 1004, in _run
result.output = self._collect_outputs()
File "/home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/venvs/dev3.9.1/lib/python3.9/site-packages/pydra/engine/core.py", line 1098, in _collect_outputs
raise ValueError(f"Task {val.name} raised an error")
ValueError: Task test raised an error
testkraken workflows4regtests/afni_dc2019/3dcopy_datalad/ 5.54s user 3.61s system 53% cpu 17.133 total
```
and works if path is absolute
```shell
(git)lena:~/.tmp/dl-kraken-yqaBPWM/testkraken[master]git
$> sudo rm -rf workflows4regtests/afni_dc2019/3dcopy_datalad/data/ ; testkraken $PWD/workflows4regtests/afni_dc2019/3dcopy_datalad/
Installing test data
[INFO ] Scanning for unlocked files (this may take some time)
[INFO ] Remote origin not usable by git-annex; setting annex-ignore
running testkraken for /home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/workflows4regtests/afni_dc2019/3dcopy_datalad/; working directory - None
+ building 1 Docker images
++ building image: {'pkg_manager': 'apt', 'instructions': (('base', 'debian:stretch'), ('afni', {'version': 'latest'}))}
Sending build context to Docker daemon 6.144kB
Step 1/9 : FROM debian:stretch
---> 62ace29a8c8f
Step 2/9 : USER root
---> Using cache
---> 0a0242cabb6b
Step 3/9 : ARG DEBIAN_FRONTEND="noninteractive"
---> Using cache
---> 9b5957f75547
Step 4/9 : ENV LANG="en_US.UTF-8" LC_ALL="en_US.UTF-8" ND_ENTRYPOINT="/neurodocker/startup.sh"
---> Using cache
---> ee7c9c814662
Step 5/9 : RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" && apt-get update -qq && apt-get install -y -q --no-install-recommends apt-utils bzip2 ca-certificates curl locales unzip && apt-get clean && rm -rf /var/lib/apt/lists/* && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && dpkg-reconfigure --frontend=noninteractive locales && update-locale LANG="en_US.UTF-8" && chmod 777 /opt && chmod a+s /opt && mkdir -p /neurodocker && if [ ! -f "$ND_ENTRYPOINT" ]; then echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" && echo 'set -e' >> "$ND_ENTRYPOINT" && echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" && echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; fi && chmod -R 777 /neurodocker && chmod a+s /neurodocker
---> Using cache
---> 2ffd82e60498
Step 6/9 : ENTRYPOINT ["/neurodocker/startup.sh"]
---> Using cache
---> fe1ff4b56fc6
Step 7/9 : ENV PATH="/opt/afni-latest:$PATH" AFNI_PLUGINPATH="/opt/afni-latest"
---> Using cache
---> d65fc11a2624
Step 8/9 : RUN apt-get update -qq && apt-get install -y -q --no-install-recommends ed gsl-bin libglib2.0-0 libglu1-mesa-dev libglw1-mesa libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb && apt-get clean && rm -rf /var/lib/apt/lists/* && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb && dpkg -i /tmp/toinstall.deb && rm /tmp/toinstall.deb && curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb && dpkg -i /tmp/toinstall.deb && rm /tmp/toinstall.deb && apt-get install -f && apt-get clean && rm -rf /var/lib/apt/lists/* && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" && if [ -n "$gsl2_path" ]; then ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; fi && ldconfig && echo "Downloading AFNI ..." && mkdir -p /opt/afni-latest && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz | tar -xz -C /opt/afni-latest --strip-components 1
---> Using cache
---> b6b2afe5a112
Step 9/9 : RUN echo '{ \n "pkg_manager": "apt", \n "instructions": [ \n [ \n "base", \n "debian:stretch" \n ], \n [ \n "afni", \n { \n "version": "latest" \n } \n ] \n ] \n}' > /neurodocker/neurodocker_specs.json
---> Using cache
---> 3e626823d1a5
Successfully built 3e626823d1a5
Successfully tagged repronim/testkraken:a1f5db7b4e67ffa4aaba1de3db1bba4f65784325
running pydra workflow for /home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/workflows4regtests/afni_dc2019/3dcopy_datalad in working directory - /home/yoh/.tmp/testkraken-3dcopy_datalad3etbyy8y
testkraken $PWD/workflows4regtests/afni_dc2019/3dcopy_datalad/ 5.93s user 3.64s system 48% cpu 19.672 total
```
djarecka
commented
3 years ago
but when I run with relative path it kabooms
```shell (git)lena:~/.tmp/dl-kraken-yqaBPWM/testkraken[master]git $> sudo rm -rf workflows4regtests/afni_dc2019/3dcopy_datalad/data/ ; testkraken workflows4regtests/afni_dc2019/3dcopy_datalad/ Installing test data [INFO ] Scanning for unlocked files (this may take some time) [INFO ] Remote origin not usable by git-annex; setting annex-ignore running testkraken for workflows4regtests/afni_dc2019/3dcopy_datalad/; working directory - None + building 1 Docker images ++ building image: {'pkg_manager': 'apt', 'instructions': (('base', 'debian:stretch'), ('afni', {'version': 'latest'}))} Sending build context to Docker daemon 6.144kB Step 1/9 : FROM debian:stretch ---> 62ace29a8c8f Step 2/9 : USER root ---> Using cache ---> 0a0242cabb6b Step 3/9 : ARG DEBIAN_FRONTEND="noninteractive" ---> Using cache ---> 9b5957f75547 Step 4/9 : ENV LANG="en_US.UTF-8" LC_ALL="en_US.UTF-8" ND_ENTRYPOINT="/neurodocker/startup.sh" ---> Using cache ---> ee7c9c814662 Step 5/9 : RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" && apt-get update -qq && apt-get install -y -q --no-install-recommends apt-utils bzip2 ca-certificates curl locales unzip && apt-get clean && rm -rf /var/lib/apt/lists/* && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && dpkg-reconfigure --frontend=noninteractive locales && update-locale LANG="en_US.UTF-8" && chmod 777 /opt && chmod a+s /opt && mkdir -p /neurodocker && if [ ! -f "$ND_ENTRYPOINT" ]; then echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" && echo 'set -e' >> "$ND_ENTRYPOINT" && echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" && echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; fi && chmod -R 777 /neurodocker && chmod a+s /neurodocker ---> Using cache ---> 2ffd82e60498 Step 6/9 : ENTRYPOINT ["/neurodocker/startup.sh"] ---> Using cache ---> fe1ff4b56fc6 Step 7/9 : ENV PATH="/opt/afni-latest:$PATH" AFNI_PLUGINPATH="/opt/afni-latest" ---> Using cache ---> d65fc11a2624 Step 8/9 : RUN apt-get update -qq && apt-get install -y -q --no-install-recommends ed gsl-bin libglib2.0-0 libglu1-mesa-dev libglw1-mesa libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb && apt-get clean && rm -rf /var/lib/apt/lists/* && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb && dpkg -i /tmp/toinstall.deb && rm /tmp/toinstall.deb && curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb && dpkg -i /tmp/toinstall.deb && rm /tmp/toinstall.deb && apt-get install -f && apt-get clean && rm -rf /var/lib/apt/lists/* && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" && if [ -n "$gsl2_path" ]; then ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; fi && ldconfig && echo "Downloading AFNI ..." && mkdir -p /opt/afni-latest && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz | tar -xz -C /opt/afni-latest --strip-components 1 ---> Using cache ---> b6b2afe5a112 Step 9/9 : RUN echo '{ \n "pkg_manager": "apt", \n "instructions": [ \n [ \n "base", \n "debian:stretch" \n ], \n [ \n "afni", \n { \n "version": "latest" \n } \n ] \n ] \n}' > /neurodocker/neurodocker_specs.json ---> Using cache ---> 3e626823d1a5 Successfully built 3e626823d1a5 Successfully tagged repronim/testkraken:a1f5db7b4e67ffa4aaba1de3db1bba4f65784325 running pydra workflow for workflows4regtests/afni_dc2019/3dcopy_datalad in working directory - /home/yoh/.tmp/testkraken-3dcopy_dataladw9ghu9rw Task exception was never retrieved future:
and works if path is absolute
```shell (git)lena:~/.tmp/dl-kraken-yqaBPWM/testkraken[master]git $> sudo rm -rf workflows4regtests/afni_dc2019/3dcopy_datalad/data/ ; testkraken $PWD/workflows4regtests/afni_dc2019/3dcopy_datalad/ Installing test data [INFO ] Scanning for unlocked files (this may take some time) [INFO ] Remote origin not usable by git-annex; setting annex-ignore running testkraken for /home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/workflows4regtests/afni_dc2019/3dcopy_datalad/; working directory - None + building 1 Docker images ++ building image: {'pkg_manager': 'apt', 'instructions': (('base', 'debian:stretch'), ('afni', {'version': 'latest'}))} Sending build context to Docker daemon 6.144kB Step 1/9 : FROM debian:stretch ---> 62ace29a8c8f Step 2/9 : USER root ---> Using cache ---> 0a0242cabb6b Step 3/9 : ARG DEBIAN_FRONTEND="noninteractive" ---> Using cache ---> 9b5957f75547 Step 4/9 : ENV LANG="en_US.UTF-8" LC_ALL="en_US.UTF-8" ND_ENTRYPOINT="/neurodocker/startup.sh" ---> Using cache ---> ee7c9c814662 Step 5/9 : RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" && apt-get update -qq && apt-get install -y -q --no-install-recommends apt-utils bzip2 ca-certificates curl locales unzip && apt-get clean && rm -rf /var/lib/apt/lists/* && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen && dpkg-reconfigure --frontend=noninteractive locales && update-locale LANG="en_US.UTF-8" && chmod 777 /opt && chmod a+s /opt && mkdir -p /neurodocker && if [ ! -f "$ND_ENTRYPOINT" ]; then echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" && echo 'set -e' >> "$ND_ENTRYPOINT" && echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" && echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; fi && chmod -R 777 /neurodocker && chmod a+s /neurodocker ---> Using cache ---> 2ffd82e60498 Step 6/9 : ENTRYPOINT ["/neurodocker/startup.sh"] ---> Using cache ---> fe1ff4b56fc6 Step 7/9 : ENV PATH="/opt/afni-latest:$PATH" AFNI_PLUGINPATH="/opt/afni-latest" ---> Using cache ---> d65fc11a2624 Step 8/9 : RUN apt-get update -qq && apt-get install -y -q --no-install-recommends ed gsl-bin libglib2.0-0 libglu1-mesa-dev libglw1-mesa libgomp1 libjpeg62 libxm4 netpbm tcsh xfonts-base xvfb && apt-get clean && rm -rf /var/lib/apt/lists/* && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb && dpkg -i /tmp/toinstall.deb && rm /tmp/toinstall.deb && curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb && dpkg -i /tmp/toinstall.deb && rm /tmp/toinstall.deb && apt-get install -f && apt-get clean && rm -rf /var/lib/apt/lists/* && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" && if [ -n "$gsl2_path" ]; then ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; fi && ldconfig && echo "Downloading AFNI ..." && mkdir -p /opt/afni-latest && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz | tar -xz -C /opt/afni-latest --strip-components 1 ---> Using cache ---> b6b2afe5a112 Step 9/9 : RUN echo '{ \n "pkg_manager": "apt", \n "instructions": [ \n [ \n "base", \n "debian:stretch" \n ], \n [ \n "afni", \n { \n "version": "latest" \n } \n ] \n ] \n}' > /neurodocker/neurodocker_specs.json ---> Using cache ---> 3e626823d1a5 Successfully built 3e626823d1a5 Successfully tagged repronim/testkraken:a1f5db7b4e67ffa4aaba1de3db1bba4f65784325 running pydra workflow for /home/yoh/.tmp/dl-kraken-yqaBPWM/testkraken/workflows4regtests/afni_dc2019/3dcopy_datalad in working directory - /home/yoh/.tmp/testkraken-3dcopy_datalad3etbyy8y testkraken $PWD/workflows4regtests/afni_dc2019/3dcopy_datalad/ 5.93s user 3.64s system 48% cpu 19.672 total ```