[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    475      0 --:--:-- --:--:-- --:--:--   476

100 28083  100 28083    0     0  70491      0 --:--:-- --:--:-- --:--:-- 70491

[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.
  - 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_environment_variable_Metin` may be invalid.
    - Variable `value_component_environment_variable_Metin` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_Met_variable_Met` may be invalid.
    - Variable `value_component_Met_variable_Met` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_AdoMet_variable_AdoMet` may be invalid.
    - Variable `value_component_AdoMet_variable_AdoMet` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_AdoHcy_variable_AdoHcy` may be invalid.
    - Variable `value_component_AdoHcy_variable_AdoHcy` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_Hcy_variable_Hcy` may be invalid.
    - Variable `value_component_Hcy_variable_Hcy` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MATI_variable_V_MATI` may be invalid.
    - Variable `value_component_V_MATI_variable_V_MATI` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MATI_variable_V_MATImax` may be invalid.
    - Variable `value_component_V_MATI_variable_V_MATImax` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MATI_variable_Km_MATI` may be invalid.
    - Variable `value_component_V_MATI_variable_Km_MATI` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MATI_variable_Ki_MATI` may be invalid.
    - Variable `value_component_V_MATI_variable_Ki_MATI` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MATIII_variable_V_MATIII` may be invalid.
    - Variable `value_component_V_MATIII_variable_V_MATIII` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MATIII_variable_V_MATIIImax` may be invalid.
    - Variable `value_component_V_MATIII_variable_V_MATIIImax` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MATIII_variable_Km1_MATIII` may be invalid.
    - Variable `value_component_V_MATIII_variable_Km1_MATIII` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MATIII_variable_Km2_MATIII` may be invalid.
    - Variable `value_component_V_MATIII_variable_Km2_MATIII` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_GNMT_variable_V_GNMT` may be invalid.
    - Variable `value_component_V_GNMT_variable_V_GNMT` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_GNMT_variable_V_GNMTmax` may be invalid.
    - Variable `value_component_V_GNMT_variable_V_GNMTmax` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_GNMT_variable_Km_GNMT` may be invalid.
    - Variable `value_component_V_GNMT_variable_Km_GNMT` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_GNMT_variable_Ki_GNMT` may be invalid.
    - Variable `value_component_V_GNMT_variable_Ki_GNMT` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_METH_variable_V_METH` may be invalid.
    - Variable `value_component_V_METH_variable_V_METH` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_METH_variable_V_METHmax` may be invalid.
    - Variable `value_component_V_METH_variable_V_METHmax` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_METH_variable_Km1_METH` may be invalid.
    - Variable `value_component_V_METH_variable_Km1_METH` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_METH_variable_Km2_METH_A` may be invalid.
    - Variable `value_component_V_METH_variable_Km2_METH_A` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MS_variable_V_MS` may be invalid.
    - Variable `value_component_V_MS_variable_V_MS` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MS_variable_five_mTHF` may be invalid.
    - Variable `value_component_V_MS_variable_five_mTHF` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MS_variable_V_MSmax` may be invalid.
    - Variable `value_component_V_MS_variable_V_MSmax` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MS_variable_Kd_MS` may be invalid.
    - Variable `value_component_V_MS_variable_Kd_MS` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MS_variable_Km_Hcy_MS` may be invalid.
    - Variable `value_component_V_MS_variable_Km_Hcy_MS` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_MS_variable_Km_five_mTHF_MS` may be invalid.
    - Variable `value_component_V_MS_variable_Km_five_mTHF_MS` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_AH_variable_V_AH` may be invalid.
    - Variable `value_component_V_AH_variable_V_AH` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_AH_variable_alpha1` may be invalid.
    - Variable `value_component_V_AH_variable_alpha1` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_AH_variable_alpha2` may be invalid.
    - Variable `value_component_V_AH_variable_alpha2` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_CBS_variable_V_CBS` may be invalid.
    - Variable `value_component_V_CBS_variable_V_CBS` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_CBS_variable_beta1` may be invalid.
    - Variable `value_component_V_CBS_variable_beta1` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_CBS_variable_beta2` may be invalid.
    - Variable `value_component_V_CBS_variable_beta2` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_BHMT_variable_V_BHMT` may be invalid.
    - Variable `value_component_V_BHMT_variable_V_BHMT` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_BHMT_variable_V_BHMTmax` may be invalid.
    - Variable `value_component_V_BHMT_variable_V_BHMTmax` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_V_BHMT_variable_Km_BHMT` may be invalid.
    - Variable `value_component_V_BHMT_variable_Km_BHMT` 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.
    - 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_environment_variable_Metin` may be invalid.
      - Variable `value_component_environment_variable_Metin` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_Met_variable_Met` may be invalid.
      - Variable `value_component_Met_variable_Met` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_AdoMet_variable_AdoMet` may be invalid.
      - Variable `value_component_AdoMet_variable_AdoMet` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_AdoHcy_variable_AdoHcy` may be invalid.
      - Variable `value_component_AdoHcy_variable_AdoHcy` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_Hcy_variable_Hcy` may be invalid.
      - Variable `value_component_Hcy_variable_Hcy` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MATI_variable_V_MATI` may be invalid.
      - Variable `value_component_V_MATI_variable_V_MATI` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MATI_variable_V_MATImax` may be invalid.
      - Variable `value_component_V_MATI_variable_V_MATImax` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MATI_variable_Km_MATI` may be invalid.
      - Variable `value_component_V_MATI_variable_Km_MATI` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MATI_variable_Ki_MATI` may be invalid.
      - Variable `value_component_V_MATI_variable_Ki_MATI` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MATIII_variable_V_MATIII` may be invalid.
      - Variable `value_component_V_MATIII_variable_V_MATIII` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MATIII_variable_V_MATIIImax` may be invalid.
      - Variable `value_component_V_MATIII_variable_V_MATIIImax` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MATIII_variable_Km1_MATIII` may be invalid.
      - Variable `value_component_V_MATIII_variable_Km1_MATIII` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MATIII_variable_Km2_MATIII` may be invalid.
      - Variable `value_component_V_MATIII_variable_Km2_MATIII` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_GNMT_variable_V_GNMT` may be invalid.
      - Variable `value_component_V_GNMT_variable_V_GNMT` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_GNMT_variable_V_GNMTmax` may be invalid.
      - Variable `value_component_V_GNMT_variable_V_GNMTmax` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_GNMT_variable_Km_GNMT` may be invalid.
      - Variable `value_component_V_GNMT_variable_Km_GNMT` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_GNMT_variable_Ki_GNMT` may be invalid.
      - Variable `value_component_V_GNMT_variable_Ki_GNMT` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_METH_variable_V_METH` may be invalid.
      - Variable `value_component_V_METH_variable_V_METH` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_METH_variable_V_METHmax` may be invalid.
      - Variable `value_component_V_METH_variable_V_METHmax` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_METH_variable_Km1_METH` may be invalid.
      - Variable `value_component_V_METH_variable_Km1_METH` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_METH_variable_Km2_METH_A` may be invalid.
      - Variable `value_component_V_METH_variable_Km2_METH_A` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MS_variable_V_MS` may be invalid.
      - Variable `value_component_V_MS_variable_V_MS` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MS_variable_five_mTHF` may be invalid.
      - Variable `value_component_V_MS_variable_five_mTHF` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MS_variable_V_MSmax` may be invalid.
      - Variable `value_component_V_MS_variable_V_MSmax` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MS_variable_Kd_MS` may be invalid.
      - Variable `value_component_V_MS_variable_Kd_MS` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MS_variable_Km_Hcy_MS` may be invalid.
      - Variable `value_component_V_MS_variable_Km_Hcy_MS` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_MS_variable_Km_five_mTHF_MS` may be invalid.
      - Variable `value_component_V_MS_variable_Km_five_mTHF_MS` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_AH_variable_V_AH` may be invalid.
      - Variable `value_component_V_AH_variable_V_AH` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_AH_variable_alpha1` may be invalid.
      - Variable `value_component_V_AH_variable_alpha1` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_AH_variable_alpha2` may be invalid.
      - Variable `value_component_V_AH_variable_alpha2` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_CBS_variable_V_CBS` may be invalid.
      - Variable `value_component_V_CBS_variable_V_CBS` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_CBS_variable_beta1` may be invalid.
      - Variable `value_component_V_CBS_variable_beta1` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_CBS_variable_beta2` may be invalid.
      - Variable `value_component_V_CBS_variable_beta2` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_BHMT_variable_V_BHMT` may be invalid.
      - Variable `value_component_V_BHMT_variable_V_BHMT` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_BHMT_variable_V_BHMTmax` may be invalid.
      - Variable `value_component_V_BHMT_variable_V_BHMTmax` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_V_BHMT_variable_Km_BHMT` may be invalid.
      - Variable `value_component_V_BHMT_variable_Km_BHMT` 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: 37 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 22.0 KiB/22.0 KiB (239.8 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261779590c6a19595579635/rawLog.txt
Completed 30.3 KiB/30.3 KiB (280.3 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/6261779590c6a19595579635/outputs/log.yml

[0;36m================================================== Zipping outputs ==================================================[0m
  adding: outputs/ (stored 0%)
