[0;36mThank you for using runBioSimulations![0m

[0;36m================================================ Loading Singularity ================================================[0m

[0;36m=================================================== Set up storage ==================================================[0m

[0;36m========================================== Downloading COMBINE/OMEX archive =========================================[0m
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   139  100   139    0     0    457      0 --:--:-- --:--:-- --:--:--   458

  0 54928    0   485    0     0   1109      0  0:00:49 --:--:--  0:00:49  1109
100 54928  100 54928    0     0   119k      0 --:--:-- --:--:-- --:--:-- 4833k

[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================[0m
INFO:    Using cached SIF image
Traceback (most recent call last):
  File "/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py", line 247, in <module>
    if not update_paths(args.path, args.scripts_dir, args.clear_args, args.extra_args):
  File "/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py", line 213, in update_paths
    update_scripts(scripts_dir, new_path, clear_args, extra_args)
  File "/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py", line 125, in update_scripts
    update_script(os.path.join(bin_dir, fn), new_path, clear_args, extra_args)
  File "/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py", line 118, in update_script
    with open(script_filename, 'w') as f:
OSError: [Errno 30] Read-only file system: '/home/opencor/OpenCOR/bin/../python/bin/biosimulators-utils'
/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mCOMBINE/OMEX archive may be invalid.
  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.[0m
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe SED document is potentially incorrect.
  - Model `model` may be invalid.
    - The changes of the model may be invalid.
      - Change 1 may be invalid.
        - XPath could not be validated.
      - Change 2 may be invalid.
        - XPath could not be validated.
      - Change 3 may be invalid.
        - XPath could not be validated.
      - Change 4 may be invalid.
        - XPath could not be validated.
      - Change 5 may be invalid.
        - XPath could not be validated.
      - Change 6 may be invalid.
        - XPath could not be validated.
      - Change 7 may be invalid.
        - XPath could not be validated.
      - Change 8 may be invalid.
        - XPath could not be validated.
      - Change 9 may be invalid.
        - XPath could not be validated.
      - Change 10 may be invalid.
        - XPath could not be validated.
      - Change 11 may be invalid.
        - XPath could not be validated.
      - Change 12 may be invalid.
        - XPath could not be validated.
      - Change 13 may be invalid.
        - XPath could not be validated.
      - Change 14 may be invalid.
        - XPath could not be validated.
      - Change 15 may be invalid.
        - XPath could not be validated.
      - Change 16 may be invalid.
        - XPath could not be validated.
      - Change 17 may be invalid.
        - XPath could not be validated.
      - Change 18 may be invalid.
        - XPath could not be validated.
      - Change 19 may be invalid.
        - XPath could not be validated.
      - Change 20 may be invalid.
        - XPath could not be validated.
      - Change 21 may be invalid.
        - XPath could not be validated.
      - Change 22 may be invalid.
        - XPath could not be validated.
      - Change 23 may be invalid.
        - XPath could not be validated.
      - Change 24 may be invalid.
        - XPath could not be validated.
      - Change 25 may be invalid.
        - XPath could not be validated.
      - Change 26 may be invalid.
        - XPath could not be validated.
      - Change 27 may be invalid.
        - XPath could not be validated.
      - Change 28 may be invalid.
        - XPath could not be validated.
      - Change 29 may be invalid.
        - XPath could not be validated.
      - Change 30 may be invalid.
        - XPath could not be validated.
  - Data generator `data_generator_value_component_environment_variable_time` may be invalid.
    - Variable `value_component_environment_variable_time` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_O2_variable_O2` may be invalid.
    - Variable `value_component_O2_variable_O2` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_O2_radical_variable_O2_radical` may be invalid.
    - Variable `value_component_O2_radical_variable_O2_radical` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_NADH_variable_NADH` may be invalid.
    - Variable `value_component_NADH_variable_NADH` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_NAD_variable_NAD` may be invalid.
    - Variable `value_component_NAD_variable_NAD` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_NAD_radical_variable_NAD_radical` may be invalid.
    - Variable `value_component_NAD_radical_variable_NAD_radical` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_NAD2_variable_NAD2` may be invalid.
    - Variable `value_component_NAD2_variable_NAD2` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_H2O2_variable_H2O2` may be invalid.
    - Variable `value_component_H2O2_variable_H2O2` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_Per3_variable_Per3` may be invalid.
    - Variable `value_component_Per3_variable_Per3` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_Per2_variable_Per2` may be invalid.
    - Variable `value_component_Per2_variable_Per2` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_coI_variable_coI` may be invalid.
    - Variable `value_component_coI_variable_coI` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_coII_variable_coII` may be invalid.
    - Variable `value_component_coII_variable_coII` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_coIII_variable_coIII` may be invalid.
    - Variable `value_component_coIII_variable_coIII` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_Ar_radical_variable_Ar_radical` may be invalid.
    - Variable `value_component_Ar_radical_variable_Ar_radical` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_ArH_variable_ArH` may be invalid.
    - Variable `value_component_ArH_variable_ArH` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v1_variable_v1` may be invalid.
    - Variable `value_component_v1_variable_v1` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v1_variable_k1` may be invalid.
    - Variable `value_component_v1_variable_k1` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v2_variable_v2` may be invalid.
    - Variable `value_component_v2_variable_v2` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v2_variable_k2` may be invalid.
    - Variable `value_component_v2_variable_k2` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v3_variable_v3` may be invalid.
    - Variable `value_component_v3_variable_v3` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v3_variable_k3` may be invalid.
    - Variable `value_component_v3_variable_k3` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v4_variable_v4` may be invalid.
    - Variable `value_component_v4_variable_v4` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v4_variable_k4` may be invalid.
    - Variable `value_component_v4_variable_k4` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v5_variable_v5` may be invalid.
    - Variable `value_component_v5_variable_v5` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v5_variable_k5` may be invalid.
    - Variable `value_component_v5_variable_k5` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v6_variable_v6` may be invalid.
    - Variable `value_component_v6_variable_v6` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v6_variable_k6` may be invalid.
    - Variable `value_component_v6_variable_k6` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v7_variable_v7` may be invalid.
    - Variable `value_component_v7_variable_v7` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v7_variable_k7` may be invalid.
    - Variable `value_component_v7_variable_k7` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v8_variable_v8` may be invalid.
    - Variable `value_component_v8_variable_v8` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v8_variable_k8` may be invalid.
    - Variable `value_component_v8_variable_k8` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v9_variable_v9` may be invalid.
    - Variable `value_component_v9_variable_v9` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v9_variable_k9` may be invalid.
    - Variable `value_component_v9_variable_k9` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v10_variable_v10` may be invalid.
    - Variable `value_component_v10_variable_v10` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v10_variable_k10` may be invalid.
    - Variable `value_component_v10_variable_k10` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v11_variable_v11` may be invalid.
    - Variable `value_component_v11_variable_v11` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v11_variable_k11` may be invalid.
    - Variable `value_component_v11_variable_k11` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v12_variable_v12` may be invalid.
    - Variable `value_component_v12_variable_v12` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v12_variable_k12` may be invalid.
    - Variable `value_component_v12_variable_k12` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v13_variable_v13` may be invalid.
    - Variable `value_component_v13_variable_v13` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v13_variable_O2eq` may be invalid.
    - Variable `value_component_v13_variable_O2eq` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v13_variable_k13` may be invalid.
    - Variable `value_component_v13_variable_k13` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v13_back_variable_v13_back` may be invalid.
    - Variable `value_component_v13_back_variable_v13_back` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v13_back_variable_k13_` may be invalid.
    - Variable `value_component_v13_back_variable_k13_` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v14_variable_v14` may be invalid.
    - Variable `value_component_v14_variable_v14` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_v14_variable_k14` may be invalid.
    - Variable `value_component_v14_variable_k14` may be invalid.
      - XPath could not be validated.[0m
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: [33mThe COMBINE/OMEX archive may be invalid.
  - The SED-ML file at location `simulation_0.sedml` may be invalid.
    - Model `model` may be invalid.
      - The changes of the model may be invalid.
        - Change 1 may be invalid.
          - XPath could not be validated.
        - Change 2 may be invalid.
          - XPath could not be validated.
        - Change 3 may be invalid.
          - XPath could not be validated.
        - Change 4 may be invalid.
          - XPath could not be validated.
        - Change 5 may be invalid.
          - XPath could not be validated.
        - Change 6 may be invalid.
          - XPath could not be validated.
        - Change 7 may be invalid.
          - XPath could not be validated.
        - Change 8 may be invalid.
          - XPath could not be validated.
        - Change 9 may be invalid.
          - XPath could not be validated.
        - Change 10 may be invalid.
          - XPath could not be validated.
        - Change 11 may be invalid.
          - XPath could not be validated.
        - Change 12 may be invalid.
          - XPath could not be validated.
        - Change 13 may be invalid.
          - XPath could not be validated.
        - Change 14 may be invalid.
          - XPath could not be validated.
        - Change 15 may be invalid.
          - XPath could not be validated.
        - Change 16 may be invalid.
          - XPath could not be validated.
        - Change 17 may be invalid.
          - XPath could not be validated.
        - Change 18 may be invalid.
          - XPath could not be validated.
        - Change 19 may be invalid.
          - XPath could not be validated.
        - Change 20 may be invalid.
          - XPath could not be validated.
        - Change 21 may be invalid.
          - XPath could not be validated.
        - Change 22 may be invalid.
          - XPath could not be validated.
        - Change 23 may be invalid.
          - XPath could not be validated.
        - Change 24 may be invalid.
          - XPath could not be validated.
        - Change 25 may be invalid.
          - XPath could not be validated.
        - Change 26 may be invalid.
          - XPath could not be validated.
        - Change 27 may be invalid.
          - XPath could not be validated.
        - Change 28 may be invalid.
          - XPath could not be validated.
        - Change 29 may be invalid.
          - XPath could not be validated.
        - Change 30 may be invalid.
          - XPath could not be validated.
    - Data generator `data_generator_value_component_environment_variable_time` may be invalid.
      - Variable `value_component_environment_variable_time` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_O2_variable_O2` may be invalid.
      - Variable `value_component_O2_variable_O2` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_O2_radical_variable_O2_radical` may be invalid.
      - Variable `value_component_O2_radical_variable_O2_radical` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_NADH_variable_NADH` may be invalid.
      - Variable `value_component_NADH_variable_NADH` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_NAD_variable_NAD` may be invalid.
      - Variable `value_component_NAD_variable_NAD` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_NAD_radical_variable_NAD_radical` may be invalid.
      - Variable `value_component_NAD_radical_variable_NAD_radical` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_NAD2_variable_NAD2` may be invalid.
      - Variable `value_component_NAD2_variable_NAD2` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_H2O2_variable_H2O2` may be invalid.
      - Variable `value_component_H2O2_variable_H2O2` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_Per3_variable_Per3` may be invalid.
      - Variable `value_component_Per3_variable_Per3` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_Per2_variable_Per2` may be invalid.
      - Variable `value_component_Per2_variable_Per2` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_coI_variable_coI` may be invalid.
      - Variable `value_component_coI_variable_coI` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_coII_variable_coII` may be invalid.
      - Variable `value_component_coII_variable_coII` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_coIII_variable_coIII` may be invalid.
      - Variable `value_component_coIII_variable_coIII` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_Ar_radical_variable_Ar_radical` may be invalid.
      - Variable `value_component_Ar_radical_variable_Ar_radical` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_ArH_variable_ArH` may be invalid.
      - Variable `value_component_ArH_variable_ArH` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v1_variable_v1` may be invalid.
      - Variable `value_component_v1_variable_v1` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v1_variable_k1` may be invalid.
      - Variable `value_component_v1_variable_k1` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v2_variable_v2` may be invalid.
      - Variable `value_component_v2_variable_v2` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v2_variable_k2` may be invalid.
      - Variable `value_component_v2_variable_k2` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v3_variable_v3` may be invalid.
      - Variable `value_component_v3_variable_v3` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v3_variable_k3` may be invalid.
      - Variable `value_component_v3_variable_k3` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v4_variable_v4` may be invalid.
      - Variable `value_component_v4_variable_v4` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v4_variable_k4` may be invalid.
      - Variable `value_component_v4_variable_k4` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v5_variable_v5` may be invalid.
      - Variable `value_component_v5_variable_v5` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v5_variable_k5` may be invalid.
      - Variable `value_component_v5_variable_k5` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v6_variable_v6` may be invalid.
      - Variable `value_component_v6_variable_v6` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v6_variable_k6` may be invalid.
      - Variable `value_component_v6_variable_k6` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v7_variable_v7` may be invalid.
      - Variable `value_component_v7_variable_v7` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v7_variable_k7` may be invalid.
      - Variable `value_component_v7_variable_k7` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v8_variable_v8` may be invalid.
      - Variable `value_component_v8_variable_v8` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v8_variable_k8` may be invalid.
      - Variable `value_component_v8_variable_k8` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v9_variable_v9` may be invalid.
      - Variable `value_component_v9_variable_v9` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v9_variable_k9` may be invalid.
      - Variable `value_component_v9_variable_k9` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v10_variable_v10` may be invalid.
      - Variable `value_component_v10_variable_v10` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v10_variable_k10` may be invalid.
      - Variable `value_component_v10_variable_k10` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v11_variable_v11` may be invalid.
      - Variable `value_component_v11_variable_v11` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v11_variable_k11` may be invalid.
      - Variable `value_component_v11_variable_k11` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v12_variable_v12` may be invalid.
      - Variable `value_component_v12_variable_v12` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v12_variable_k12` may be invalid.
      - Variable `value_component_v12_variable_k12` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v13_variable_v13` may be invalid.
      - Variable `value_component_v13_variable_v13` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v13_variable_O2eq` may be invalid.
      - Variable `value_component_v13_variable_O2eq` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v13_variable_k13` may be invalid.
      - Variable `value_component_v13_variable_k13` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v13_back_variable_v13_back` may be invalid.
      - Variable `value_component_v13_back_variable_v13_back` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v13_back_variable_k13_` may be invalid.
      - Variable `value_component_v13_back_variable_k13_` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v14_variable_v14` may be invalid.
      - Variable `value_component_v14_variable_v14` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_v14_variable_k14` may be invalid.
      - Variable `value_component_v14_variable_k14` may be invalid.
        - XPath could not be validated.[0m
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:
  simulation_0.sedml:
    Tasks (1):
      task
    Reports (1):
      report: 46 data sets

Executing SED-ML file 1: simulation_0.sedml ...

Bundling outputs ...
Cleaning up ...

============= SUMMARY =============
Executed 1 SED documents:
  SED documents (1):
    Succeeded: 1
    Skipped: 0
    Failed: 0
  Tasks (1):
    Succeeded: 1
    Skipped: 0
    Failed: 0
  Outputs (1):
    Succeeded: 1
    Skipped: 0
    Failed: 0


[0;36m===================================================== Saving log ====================================================[0m
Completed 25.4 KiB/25.4 KiB (296.6 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261770190c6a195955792ea/rawLog.txt
Completed 35.2 KiB/35.2 KiB (335.7 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/6261770190c6a195955792ea/outputs/log.yml

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