[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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   139  100   139    0     0    477      0 --:--:-- --:--:-- --:--:--   476

100  231k  100  231k    0     0   507k      0 --:--:-- --:--:-- --:--:--  507k

[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_B0_variable_B0` may be invalid.
    - Variable `value_component_B0_variable_B0` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_B1_variable_B1` may be invalid.
    - Variable `value_component_B1_variable_B1` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_B2_variable_B2` may be invalid.
    - Variable `value_component_B2_variable_B2` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_B3_variable_B3` may be invalid.
    - Variable `value_component_B3_variable_B3` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_B4_variable_B4` may be invalid.
    - Variable `value_component_B4_variable_B4` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_B5_variable_B5` may be invalid.
    - Variable `value_component_B5_variable_B5` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_B6_variable_B6` may be invalid.
    - Variable `value_component_B6_variable_B6` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_B7_variable_B7` may be invalid.
    - Variable `value_component_B7_variable_B7` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_B8_variable_B8` may be invalid.
    - Variable `value_component_B8_variable_B8` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_B9_variable_B9` may be invalid.
    - Variable `value_component_B9_variable_B9` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_B10_variable_B10` may be invalid.
    - Variable `value_component_B10_variable_B10` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_centroblasts_sum_variable_B_sum` may be invalid.
    - Variable `value_component_centroblasts_sum_variable_B_sum` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_C_variable_C` may be invalid.
    - Variable `value_component_C_variable_C` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_C_variable_d` may be invalid.
    - Variable `value_component_C_variable_d` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_C_star_variable_C_star` may be invalid.
    - Variable `value_component_C_star_variable_C_star` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_centrocytes_sum_variable_C_starsum` may be invalid.
    - Variable `value_component_centrocytes_sum_variable_C_starsum` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_M_variable_M` may be invalid.
    - Variable `value_component_M_variable_M` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_A_variable_A` may be invalid.
    - Variable `value_component_A_variable_A` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_A_variable_z` may be invalid.
    - Variable `value_component_A_variable_z` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_A_variable_u` may be invalid.
    - Variable `value_component_A_variable_u` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_A_variable_log_A` may be invalid.
    - Variable `value_component_A_variable_log_A` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_T_variable_T` may be invalid.
    - Variable `value_component_T_variable_T` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_T_variable_p` may be invalid.
    - Variable `value_component_T_variable_p` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_T_variable_sigma` may be invalid.
    - Variable `value_component_T_variable_sigma` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_T_variable_delta_T` may be invalid.
    - Variable `value_component_T_variable_delta_T` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_CA_variable_CA` may be invalid.
    - Variable `value_component_CA_variable_CA` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_CA_variable_SA` may be invalid.
    - Variable `value_component_CA_variable_SA` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_CT_star_variable_CT_star` may be invalid.
    - Variable `value_component_CT_star_variable_CT_star` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_CT_star_variable_ST` may be invalid.
    - Variable `value_component_CT_star_variable_ST` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_alpha_B_variable_alpha_B` may be invalid.
    - Variable `value_component_alpha_B_variable_alpha_B` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_alpha_B_variable_KB` may be invalid.
    - Variable `value_component_alpha_B_variable_KB` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_alpha_T_variable_alpha_T` may be invalid.
    - Variable `value_component_alpha_T_variable_alpha_T` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_alpha_T_variable_KT` may be invalid.
    - Variable `value_component_alpha_T_variable_KT` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_total_variable_total` may be invalid.
    - Variable `value_component_total_variable_total` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_total_variable_log_total` may be invalid.
    - Variable `value_component_total_variable_log_total` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_kinetic_parameters_variable_rho` may be invalid.
    - Variable `value_component_kinetic_parameters_variable_rho` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_kinetic_parameters_variable_mu` may be invalid.
    - Variable `value_component_kinetic_parameters_variable_mu` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_kinetic_parameters_variable_delta_B` may be invalid.
    - Variable `value_component_kinetic_parameters_variable_delta_B` may be invalid.
      - XPath could not be validated.
  - Data generator `data_generator_value_component_kinetic_parameters_variable_pr` may be invalid.
    - Variable `value_component_kinetic_parameters_variable_pr` 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_B0_variable_B0` may be invalid.
      - Variable `value_component_B0_variable_B0` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_B1_variable_B1` may be invalid.
      - Variable `value_component_B1_variable_B1` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_B2_variable_B2` may be invalid.
      - Variable `value_component_B2_variable_B2` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_B3_variable_B3` may be invalid.
      - Variable `value_component_B3_variable_B3` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_B4_variable_B4` may be invalid.
      - Variable `value_component_B4_variable_B4` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_B5_variable_B5` may be invalid.
      - Variable `value_component_B5_variable_B5` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_B6_variable_B6` may be invalid.
      - Variable `value_component_B6_variable_B6` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_B7_variable_B7` may be invalid.
      - Variable `value_component_B7_variable_B7` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_B8_variable_B8` may be invalid.
      - Variable `value_component_B8_variable_B8` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_B9_variable_B9` may be invalid.
      - Variable `value_component_B9_variable_B9` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_B10_variable_B10` may be invalid.
      - Variable `value_component_B10_variable_B10` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_centroblasts_sum_variable_B_sum` may be invalid.
      - Variable `value_component_centroblasts_sum_variable_B_sum` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_C_variable_C` may be invalid.
      - Variable `value_component_C_variable_C` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_C_variable_d` may be invalid.
      - Variable `value_component_C_variable_d` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_C_star_variable_C_star` may be invalid.
      - Variable `value_component_C_star_variable_C_star` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_centrocytes_sum_variable_C_starsum` may be invalid.
      - Variable `value_component_centrocytes_sum_variable_C_starsum` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_M_variable_M` may be invalid.
      - Variable `value_component_M_variable_M` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_A_variable_A` may be invalid.
      - Variable `value_component_A_variable_A` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_A_variable_z` may be invalid.
      - Variable `value_component_A_variable_z` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_A_variable_u` may be invalid.
      - Variable `value_component_A_variable_u` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_A_variable_log_A` may be invalid.
      - Variable `value_component_A_variable_log_A` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_T_variable_T` may be invalid.
      - Variable `value_component_T_variable_T` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_T_variable_p` may be invalid.
      - Variable `value_component_T_variable_p` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_T_variable_sigma` may be invalid.
      - Variable `value_component_T_variable_sigma` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_T_variable_delta_T` may be invalid.
      - Variable `value_component_T_variable_delta_T` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_CA_variable_CA` may be invalid.
      - Variable `value_component_CA_variable_CA` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_CA_variable_SA` may be invalid.
      - Variable `value_component_CA_variable_SA` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_CT_star_variable_CT_star` may be invalid.
      - Variable `value_component_CT_star_variable_CT_star` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_CT_star_variable_ST` may be invalid.
      - Variable `value_component_CT_star_variable_ST` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_alpha_B_variable_alpha_B` may be invalid.
      - Variable `value_component_alpha_B_variable_alpha_B` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_alpha_B_variable_KB` may be invalid.
      - Variable `value_component_alpha_B_variable_KB` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_alpha_T_variable_alpha_T` may be invalid.
      - Variable `value_component_alpha_T_variable_alpha_T` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_alpha_T_variable_KT` may be invalid.
      - Variable `value_component_alpha_T_variable_KT` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_total_variable_total` may be invalid.
      - Variable `value_component_total_variable_total` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_total_variable_log_total` may be invalid.
      - Variable `value_component_total_variable_log_total` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_kinetic_parameters_variable_rho` may be invalid.
      - Variable `value_component_kinetic_parameters_variable_rho` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_kinetic_parameters_variable_mu` may be invalid.
      - Variable `value_component_kinetic_parameters_variable_mu` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_kinetic_parameters_variable_delta_B` may be invalid.
      - Variable `value_component_kinetic_parameters_variable_delta_B` may be invalid.
        - XPath could not be validated.
    - Data generator `data_generator_value_component_kinetic_parameters_variable_pr` may be invalid.
      - Variable `value_component_kinetic_parameters_variable_pr` 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: 40 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 23.4 KiB/23.4 KiB (251.9 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/626175c790c6a19595578d38/rawLog.txt
Completed 32.0 KiB/32.0 KiB (292.6 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/626175c790c6a19595578d38/outputs/log.yml

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