Summary of what happened:
Hello,
I am trying to run cpac for the first time to do preprocessing with a custom pipeline_config.yml file, I am using ubuntu without sudo priviliges, and using cpac together with singularity.
When I run cpac run it produces an error related to instance not found.
note that in the command below, /ritter/share/data/HBN/EEG/BIDS/release_1 is a directory that follows BIDS format.
and /home/ammar/git_repos/test_cpac is also the folder where I pulled the singularity image and where I have my pipeline_config.yml file.
finally, please note that running cpac run --help produces the same error, plus some errors because I do not have docker, which can be ommited if I use cpac run --platform singularity --help
I am not sure which parts are relevant, so I tried to provide you with a full picture.
thanks in advance for help, it is much appreciated.
Command used (and if a helper script was used, a link to the helper script or the command generated):
cpac run /ritter/share/data/HBN/EEG/BIDS/release_1 /home/ammar/cpac_outputs participant --pipeline-file /home/ammar/git_repos/test_cpac/pipeline_config.yml --platform singularity
Version:
cpac version 1.8.6
Environment (Singularity):
running CPAC with cpac, installed cpac using pip install cpac without sudo previliges, and asked the admin to install singularity.
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Loading â Singularity
singularity pull --name /home/ammar/git_repos/test_cpac/c-pac:latest.sif docker://fcpindi/c-pac:latest
/usr/share/modules/init/bash: line 58: export: _moduleraw: not a function
/usr/share/modules/init/bash: line 58: export: _moduleraw: not a function
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
ERROR: Image file exists, not overwriting.
/usr/share/modules/init/bash: line 58: export: _moduleraw: not a function
/usr/share/modules/init/bash: line 58: export: _moduleraw: not a function
WARNING: pull for Docker Hub is not guaranteed to produce the
WARNING: same image on repeated pull. Use Singularity Registry
WARNING: (shub://) to pull exactly equivalent images.
ERROR: Image file exists, not overwriting.
/home/ammar/git_repos/test_cpac/c-pac:latest.sif
Loading â /home/ammar/git_repos/test_cpac/c-pac:latest.sif as "ammar (3037)" with these directory bindings:
local Singularity mode
------------------------------------------ ------------------------------------------ ------
/etc/passwd /etc/passwd ro
/home/ammar/.cpac /home/ammar/.cpac rw
/home/ammar/git_repos/test_cpac/pipeline_c /home/ammar/git_repos/test_cpac/pipeline_c ro
onfig.yml onfig.yml
/home/ammar/git_repos/test_cpac /home/ammar/git_repos/test_cpac rw
/home/ammar/cpac_outputs /home/ammar/cpac_outputs rw
/ritter/share/data/HBN/EEG/BIDS/release_1 /ritter/share/data/HBN/EEG/BIDS/release_1 ro
/home/ammar/git_repos/test_cpac/log /home/ammar/git_repos/test_cpac/log rw
/home/ammar/git_repos/test_cpac/working /home/ammar/git_repos/test_cpac/working rw
/home/ammar/git_repos/test_cpac/outputs /home/ammar/git_repos/test_cpac/outputs rw
Logging messages will refer to the Singularity paths.
No instances found.
singularity run -B /etc/passwd:/etc/passwd:ro,/home/ammar/.cpac:/home/ammar/.cpac:rw,/home/ammar/git_repos/test_cpac/pipeline_config.yml:/home/ammar/git_repos/test_cpac/pipeline_config.yml:ro,/home/ammar/git_repos/test_cpac:/home/ammar/git_repos/test_cpac:rw,/home/ammar/cpac_outputs:/home/ammar/cpac_outputs:rw,/ritter/share/data/HBN/EEG/BIDS/release_1:/ritter/share/data/HBN/EEG/BIDS/release_1:ro,/home/ammar/git_repos/test_cpac/log:/home/ammar/git_repos/test_cpac/log:rw,/home/ammar/git_repos/test_cpac/working:/home/ammar/git_repos/test_cpac/working:rw,/home/ammar/git_repos/test_cpac/outputs:/home/ammar/git_repos/test_cpac/outputs:rw instance://expensive-frito-1989 /ritter/share/data/HBN/EEG/BIDS/release_1 /home/ammar/cpac_outputs participant --pipeline-file /home/ammar/git_repos/test_cpac/pipeline_config.yml
ERROR: A daemon process is not running with this name: expensive-frito-1989
ABORT: Aborting with RETVAL=255
Traceback (most recent call last):
File "/home/ammar/anaconda3/bin/cpac", line 8, in <module>
sys.exit(run())
File "/home/ammar/anaconda3/lib/python3.10/site-packages/cpac/__main__.py", line 445, in run
main(parsed)
File "/home/ammar/anaconda3/lib/python3.10/site-packages/cpac/__main__.py", line 347, in main
Backends(**arg_vars).run(flags=args.extra_args, **arg_vars)
File "/home/ammar/anaconda3/lib/python3.10/site-packages/cpac/backends/singularity.py", line 165, in run
[
File "/home/ammar/anaconda3/lib/python3.10/site-packages/cpac/backends/singularity.py", line 165, in <listcomp>
[
File "/home/ammar/anaconda3/lib/python3.10/site-packages/cpac/backends/singularity.py", line 149, in _try_to_stream
for line in self.container:
File "/home/ammar/anaconda3/lib/python3.10/site-packages/spython/utils/terminal.py", line 155, in stream_command
raise subprocess.CalledProcessError(return_code, cmd)
subprocess.CalledProcessError: Command '['singularity', 'run', '-B', '/etc/passwd:/etc/passwd:ro,/home/ammar/.cpac:/home/ammar/.cpac:rw,/home/ammar/git_repos/test_cpac/pipeline_config.yml:/home/ammar/git_repos/test_cpac/pipeline_config.yml:ro,/home/ammar/git_repos/test_cpac:/home/ammar/git_repos/test_cpac:rw,/home/ammar/cpac_outputs:/home/ammar/cpac_outputs:rw,/ritter/share/data/HBN/EEG/BIDS/release_1:/ritter/share/data/HBN/EEG/BIDS/release_1:ro,/home/ammar/git_repos/test_cpac/log:/home/ammar/git_repos/test_cpac/log:rw,/home/ammar/git_repos/test_cpac/working:/home/ammar/git_repos/test_cpac/working:rw,/home/ammar/git_repos/test_cpac/outputs:/home/ammar/git_repos/test_cpac/outputs:rw', 'instance://expensive-frito-1989', '/ritter/share/data/HBN/EEG/BIDS/release_1', '/home/ammar/cpac_outputs', 'participant', '--pipeline-file', '/home/ammar/git_repos/test_cpac/pipeline_config.yml']' returned non-zero exit status 255.
Can you check if youâre able to open a container like