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馃悰: Vcell Simulations Failing #4134

Closed
1 task done
bilalshaikh42 opened this issue Feb 5, 2022 · 1 comment
Closed
1 task done

馃悰: Vcell Simulations Failing #4134

bilalshaikh42 opened this issue Feb 5, 2022 · 1 comment
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bug Something isn't working
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馃悰 Triage

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@bilalshaikh42
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No response

Location

runBiosimulations

What happened?

Seems vcell image has a regression with the logs issue in #4075

What made it happen?

Submitted vcell examples
FAILED 61fd6f3f8edd56f301e6a042 --- Iron distribution (Parmar et al., BMC Syst Biol, 2017; SBML; CVODE; VCell)
FAILED 61fd6f518c1e3dc95a797876 --- Repressilator (Elowitz & Leibler, Nature, 2000; SBML; CVODE; VCell)
FAILED 61fd6f57f499ccf25faaf4dd --- Tumor-suppressive oscillations (Caravagna et al., J Theor Biol, 2010; SBML; CVODE; VCell)
FAILED 61fd6f43f499ccf25faaf4aa --- Morphogenesis checkpoint (Ciliberto et al., J Cell Biol, 2003; SBML; CVODE; VCell)

Version

Production (Deployed on a .org domain)

What browsers are you seeing the problem on?

No response

Relevant log output

Running simulation task_1_simulation 1, 415 ms
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 127, in update_task_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Failed updating task status YAML
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 216, in set_output_message
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
-----------------------------------------------------------------------------------------------------
Failed updating task status YAML
Ran 1 simulations for 1 biomodels.
Ignoring unsupported output `Figure_3a` while CSV generation.
Ignoring unsupported output `Figure_3b` while CSV generation.
Ignoring unsupported output `Figure_3c` while CSV generation.
Ignoring unsupported output `Figure_3d` while CSV generation.
Generating report `report`.
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Generating report `__plot__Figure_3a`.
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Generating report `__plot__Figure_3b`.
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Generating report `__plot__Figure_3c`.
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Generating report `__plot__Figure_3d`.
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 171, in update_dataset_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
report   :  /root/outputs/./simulation_1.sedml/report.csv
HDF conversion successful
Archiving resultant PDF files to `plots.zip`.
Archiving resultant CSV files to `reports.zip`.
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 216, in set_output_message
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Failed updating task status YAML
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 150, in update_sedml_doc_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Failed updating sedml document status YAML
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 162, in update_omex_status
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Traceback (most recent call last):
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 270, in 
    fire.Fire({
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire
    component_trace = _Fire(component, args, parsed_flag_args, context, name)
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire
    component, remaining_args = _CallAndUpdateTrace(
  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace
    component = fn(*varargs, **kwargs)
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 216, in set_output_message
    yaml_dict = get_yaml_as_str(os.path.join(out_dir, "log.yml"))
  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 107, in get_yaml_as_str
    with open(yaml_path, 'r') as sy:
FileNotFoundError: [Errno 2] No such file or directory: '/root/outputs/log.yml'
Failed updating task status YAML

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@bilalshaikh42 bilalshaikh42 added the bug Something isn't working label Feb 5, 2022
@github-actions github-actions bot added this to Needs triage in 馃悰 Triage Feb 5, 2022
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bilalshaikh42 commented Feb 5, 2022 •
edited

Manually set validation to false for vcell

馃悰 Triage automation moved this from Needs triage to Closed Feb 8, 2022
@bilalshaikh42 bilalshaikh42 mentioned this issue Feb 11, 2022
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