[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    472      0 --:--:-- --:--:-- --:--:--   474

  0 1027k    0   481    0     0   1223      0  0:14:20 --:--:--  0:14:20  1223
100 1027k  100 1027k    0     0  2392k      0 --:--:-- --:--:-- --:--:-- 27.8M

[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.
  - 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_uninfected_variable_lambda` may be invalid.
    - Variable `value_component_uninfected_variable_lambda` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_uninfected_variable_d_T` may be invalid.
    - Variable `value_component_uninfected_variable_d_T` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_uninfected_variable_k` may be invalid.
    - Variable `value_component_uninfected_variable_k` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_uninfected_variable_T` may be invalid.
    - Variable `value_component_uninfected_variable_T` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_latently_infected_variable_eta` may be invalid.
    - Variable `value_component_latently_infected_variable_eta` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_latently_infected_variable_d_0` may be invalid.
    - Variable `value_component_latently_infected_variable_d_0` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_latently_infected_variable_a` may be invalid.
    - Variable `value_component_latently_infected_variable_a` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_latently_infected_variable_rho` may be invalid.
    - Variable `value_component_latently_infected_variable_rho` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_latently_infected_variable_L_0` may be invalid.
    - Variable `value_component_latently_infected_variable_L_0` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_activated_variable_p` may be invalid.
    - Variable `value_component_activated_variable_p` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_activated_variable_a_L` may be invalid.
    - Variable `value_component_activated_variable_a_L` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_activated_variable_T_off` may be invalid.
    - Variable `value_component_activated_variable_T_off` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_activated_variable_T_on` may be invalid.
    - Variable `value_component_activated_variable_T_on` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_activated_variable_f` may be invalid.
    - Variable `value_component_activated_variable_f` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_activated_variable_L_a` may be invalid.
    - Variable `value_component_activated_variable_L_a` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_productively_infected_variable_delta` may be invalid.
    - Variable `value_component_productively_infected_variable_delta` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_productively_infected_variable_T_star` may be invalid.
    - Variable `value_component_productively_infected_variable_T_star` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_viral_load_variable_p_v` may be invalid.
    - Variable `value_component_viral_load_variable_p_v` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_viral_load_variable_c` may be invalid.
    - Variable `value_component_viral_load_variable_c` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_viral_load_variable_V` may be invalid.
    - Variable `value_component_viral_load_variable_V` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_drug_efficacy_variable_efficacy` may be invalid.
    - Variable `value_component_drug_efficacy_variable_efficacy` 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 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.
  - 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_uninfected_variable_lambda` may be invalid.
    - Variable `value_component_uninfected_variable_lambda` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_uninfected_variable_d_T` may be invalid.
    - Variable `value_component_uninfected_variable_d_T` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_uninfected_variable_k` may be invalid.
    - Variable `value_component_uninfected_variable_k` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_uninfected_variable_T` may be invalid.
    - Variable `value_component_uninfected_variable_T` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_latently_infected_variable_d_0` may be invalid.
    - Variable `value_component_latently_infected_variable_d_0` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_latently_infected_variable_a_L` may be invalid.
    - Variable `value_component_latently_infected_variable_a_L` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_latently_infected_variable_eta` may be invalid.
    - Variable `value_component_latently_infected_variable_eta` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_latently_infected_variable_L` may be invalid.
    - Variable `value_component_latently_infected_variable_L` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_productively_infected_variable_delta` may be invalid.
    - Variable `value_component_productively_infected_variable_delta` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_productively_infected_variable_T_star` may be invalid.
    - Variable `value_component_productively_infected_variable_T_star` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_viral_load_variable_N` may be invalid.
    - Variable `value_component_viral_load_variable_N` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_viral_load_variable_c` may be invalid.
    - Variable `value_component_viral_load_variable_c` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_viral_load_variable_V` may be invalid.
    - Variable `value_component_viral_load_variable_V` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_drug_efficacy_variable_efficacy` may be invalid.
    - Variable `value_component_drug_efficacy_variable_efficacy` 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.
    - 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_uninfected_variable_lambda` may be invalid.
      - Variable `value_component_uninfected_variable_lambda` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_uninfected_variable_d_T` may be invalid.
      - Variable `value_component_uninfected_variable_d_T` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_uninfected_variable_k` may be invalid.
      - Variable `value_component_uninfected_variable_k` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_uninfected_variable_T` may be invalid.
      - Variable `value_component_uninfected_variable_T` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_latently_infected_variable_eta` may be invalid.
      - Variable `value_component_latently_infected_variable_eta` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_latently_infected_variable_d_0` may be invalid.
      - Variable `value_component_latently_infected_variable_d_0` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_latently_infected_variable_a` may be invalid.
      - Variable `value_component_latently_infected_variable_a` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_latently_infected_variable_rho` may be invalid.
      - Variable `value_component_latently_infected_variable_rho` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_latently_infected_variable_L_0` may be invalid.
      - Variable `value_component_latently_infected_variable_L_0` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_activated_variable_p` may be invalid.
      - Variable `value_component_activated_variable_p` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_activated_variable_a_L` may be invalid.
      - Variable `value_component_activated_variable_a_L` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_activated_variable_T_off` may be invalid.
      - Variable `value_component_activated_variable_T_off` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_activated_variable_T_on` may be invalid.
      - Variable `value_component_activated_variable_T_on` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_activated_variable_f` may be invalid.
      - Variable `value_component_activated_variable_f` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_activated_variable_L_a` may be invalid.
      - Variable `value_component_activated_variable_L_a` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_productively_infected_variable_delta` may be invalid.
      - Variable `value_component_productively_infected_variable_delta` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_productively_infected_variable_T_star` may be invalid.
      - Variable `value_component_productively_infected_variable_T_star` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_viral_load_variable_p_v` may be invalid.
      - Variable `value_component_viral_load_variable_p_v` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_viral_load_variable_c` may be invalid.
      - Variable `value_component_viral_load_variable_c` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_viral_load_variable_V` may be invalid.
      - Variable `value_component_viral_load_variable_V` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_drug_efficacy_variable_efficacy` may be invalid.
      - Variable `value_component_drug_efficacy_variable_efficacy` may be invalid.
        - XPath could not be validated.
  - The SED-ML file at location `simulation_1.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.
    - 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_uninfected_variable_lambda` may be invalid.
      - Variable `value_component_uninfected_variable_lambda` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_uninfected_variable_d_T` may be invalid.
      - Variable `value_component_uninfected_variable_d_T` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_uninfected_variable_k` may be invalid.
      - Variable `value_component_uninfected_variable_k` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_uninfected_variable_T` may be invalid.
      - Variable `value_component_uninfected_variable_T` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_latently_infected_variable_d_0` may be invalid.
      - Variable `value_component_latently_infected_variable_d_0` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_latently_infected_variable_a_L` may be invalid.
      - Variable `value_component_latently_infected_variable_a_L` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_latently_infected_variable_eta` may be invalid.
      - Variable `value_component_latently_infected_variable_eta` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_latently_infected_variable_L` may be invalid.
      - Variable `value_component_latently_infected_variable_L` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_productively_infected_variable_delta` may be invalid.
      - Variable `value_component_productively_infected_variable_delta` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_productively_infected_variable_T_star` may be invalid.
      - Variable `value_component_productively_infected_variable_T_star` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_viral_load_variable_N` may be invalid.
      - Variable `value_component_viral_load_variable_N` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_viral_load_variable_c` may be invalid.
      - Variable `value_component_viral_load_variable_c` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_viral_load_variable_V` may be invalid.
      - Variable `value_component_viral_load_variable_V` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_drug_efficacy_variable_efficacy` may be invalid.
      - Variable `value_component_drug_efficacy_variable_efficacy` may be invalid.
        - XPath could not be validated.[0m
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
Archive contains 2 SED-ML documents with 2 models, 2 simulations, 2 tasks, 2 reports, and 0 plots:
  simulation_0.sedml:
    Tasks (1):
      task
    Reports (1):
      report: 22 data sets
  simulation_1.sedml:
    Tasks (1):
      task
    Reports (1):
      report: 15 data sets

Executing SED-ML file 1: simulation_0.sedml ...
Executing SED-ML file 2: simulation_1.sedml ...

Bundling outputs ...
Cleaning up ...

============= SUMMARY =============
Executed 2 SED documents:
  SED documents (2):
    Succeeded: 2
    Skipped: 0
    Failed: 0
  Tasks (2):
    Succeeded: 2
    Skipped: 0
    Failed: 0
  Outputs (2):
    Succeeded: 2
    Skipped: 0
    Failed: 0


[0;36m===================================================== Saving log ====================================================[0m
Completed 24.5 KiB/24.5 KiB (182.8 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626177994679625b3246fa80/rawLog.txt
Completed 34.4 KiB/34.4 KiB (289.2 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/626177994679625b3246fa80/outputs/log.yml

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