[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
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[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.
  - Output `plot1` may be invalid.
    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.
  - Output `plot2` may be invalid.
    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.
  - Output `plot3` may be invalid.
    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.
  - Output `plot4` may be invalid.
    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.
  - Output `plot5` may be invalid.
    - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[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 `chen_calzone_csikasznagy_cross_novak_tyson_2004_Fig2.sedml` may be invalid.
    - Output `plot1` may be invalid.
      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.
    - Output `plot2` may be invalid.
      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.
    - Output `plot3` may be invalid.
      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.
    - Output `plot4` may be invalid.
      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.
    - Output `plot5` may be invalid.
      - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.[0m
  warnings.warn(termcolor.colored(message, Colors.warning.value), category)
Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 0 reports, and 5 plots:
  chen_calzone_csikasznagy_cross_novak_tyson_2004_Fig2.sedml:
    Tasks (2):
      repeatedTask
      task1
    Plots (5):
      plot1: 3 curves
      plot2: 3 curves
      plot3: 3 curves
      plot4: 3 curves
      plot5: 3 curves

Executing SED-ML file 1: chen_calzone_csikasznagy_cross_novak_tyson_2004_Fig2.sedml ...

Bundling outputs ...
Cleaning up ...

============= SUMMARY =============
Executed 1 SED documents:
  SED documents (1):
    Succeeded: 1
    Skipped: 0
    Failed: 0
  Tasks (2):
    Succeeded: 2
    Skipped: 0
    Failed: 0
  Outputs (5):
    Succeeded: 5
    Skipped: 0
    Failed: 0


[0;36m===================================================== Saving log ====================================================[0m
Completed 5.9 KiB/5.9 KiB (49.6 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261742c4679625b3246e393/rawLog.txt
Completed 15.0 KiB/15.0 KiB (129.0 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/6261742c4679625b3246e393/outputs/log.yml

[0;36m================================================== Zipping outputs ==================================================[0m
  adding: outputs/ (stored 0%)
  adding: outputs/log.yml (deflated 87%)
  adding: outputs/chen_calzone_csikasznagy_cross_novak_tyson_2004_Fig2.sedml/ (stored 0%)
  adding: outputs/chen_calzone_csikasznagy_cross_novak_tyson_2004_Fig2.sedml/plot3.pdf (deflated 19%)
  adding: outputs/chen_calzone_csikasznagy_cross_novak_tyson_2004_Fig2.sedml/plot4.pdf (deflated 21%)
  adding: outputs/chen_calzone_csikasznagy_cross_novak_tyson_2004_Fig2.sedml/plot5.pdf (deflated 19%)
  adding: outputs/chen_calzone_csikasznagy_cross_novak_tyson_2004_Fig2.sedml/plot2.pdf (deflated 23%)
  adding: outputs/chen_calzone_csikasznagy_cross_novak_tyson_2004_Fig2.sedml/plot1.pdf (deflated 25%)
  adding: outputs/reports.h5 (deflated 15%)
