🐛 "Argument list too long: '/bin/sh'"

[shnizzedy]

Describe the bug

Node: cpac_sub-A00023510_ses-DS2.merge_func_to_standard_139
Working directory: /output/working/cpac_sub-A00023510_ses-DS2/_scan_rest_acq-645/merge_func_to_standard_139

Node inputs:

args = <undefined>
dimension = t
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
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merged_file = <undefined>
output_type = NIFTI_GZ
tr = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 46, in run
    node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 812, in _run_interface
    runtime = run_command(runtime, output=self.terminal_output)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/utils/subprocess.py", line 110, in run_command
    close_fds=(not sys.platform.startswith("win")),
  File "/usr/local/miniconda/lib/python3.7/subprocess.py", line 800, in __init__
    restore_signals, start_new_session)
  File "/usr/local/miniconda/lib/python3.7/subprocess.py", line 1551, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
OSError: [Errno 7] Argument list too long: '/bin/sh'

To reproduce

1. Go to https://brainlife.io/app/5f3593e84615e04651bf9364
2. Click
3. Select project, anat & func inputs and enh/allow-links branch
4. Click
5. Let it run until it crashes with this error

Expected behavior

The run completes without error

Acceptance criteria

Either

• the argument length limit is increased
  or
• the merge is broken into multiple steps before the limit is exceeded
  or
• revert this step to relative paths or links?

Screenshots

Setup

C-PAC version

v1.8.1-dev ― enh/allow-links branch

Container platform

Singularity

Docker and/or Singularity version(s)

No response

Additional context

No response