{"status":"FAILED","exception":{"type":"ModuleNotFoundError","message":"No module named 'libsbml'"},"skipReason":null,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m=================================================== Set up storage ==================================================\u001b[0m\n\n\u001b[0;36m========================================== Downloading COMBINE/OMEX archive =========================================\u001b[0m\n  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n                                 Dload  Upload   Total   Spent    Left  Speed\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    461      0 --:--:-- --:--:-- --:--:--   461\n\r100  9542  100  9542    0     0  22946      0 --:--:-- --:--:-- --:--:-- 22946\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\nTraceback (most recent call last):\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 247, in <module>\n    if not update_paths(args.path, args.scripts_dir, args.clear_args, args.extra_args):\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 213, in update_paths\n    update_scripts(scripts_dir, new_path, clear_args, extra_args)\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 125, in update_scripts\n    update_script(os.path.join(bin_dir, fn), new_path, clear_args, extra_args)\n  File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 118, in update_script\n    with open(script_filename, 'w') as f:\nOSError: [Errno 30] Read-only file system: '/home/opencor/OpenCOR/bin/../python/bin/biosimulators-utils'\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: SedmlFeatureNotSupportedWarning: \u001b[33m`/tmp/tmp12_0bvak/./Adlung2021 _model_jakstat_pa.sedml` is encoded using L1V4. Only features available in L1V3 are supported. Newer features such as simple repeated tasks are not yet supported.\u001b[0m\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n\u001b[31mNo module named 'libsbml'\u001b[0m\nsrun: error: xanadu-73: task 0: Exited with exit code 1\nsrun: Terminating job step 8658237.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 2.4 KiB/2.4 KiB (32.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc726261553b9bc253f92/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 584 Bytes/584 Bytes (6.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/674dc726261553b9bc253f92/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 32%)\n  adding: rawLog.txt (deflated 66%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 3.4 KiB/5.2 KiB (30.0 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc726261553b9bc253f92/rawLog.txt\nCompleted 3.4 KiB/5.2 KiB (30.0 KiB/s) with 1 file(s) remaining\rCompleted 5.2 KiB/5.2 KiB (18.2 KiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/674dc726261553b9bc253f92/output.zip\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/manifest.xml   \n  inflating: contents/Adlung2021 _model_jakstat_pa.sedml  \n  inflating: contents/Adlung2021 _model_jakstat_pa.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 101.3 KiB/141.4 KiB (1011.9 KiB/s) with 3 file(s) remaining\rupload: contents/Adlung2021 _model_jakstat_pa.xml to s3://files.biosimulations.org/simulations/674dc726261553b9bc253f92/contents/Adlung2021 _model_jakstat_pa.xml\nCompleted 101.3 KiB/141.4 KiB (1011.9 KiB/s) with 2 file(s) remaining\rCompleted 102.0 KiB/141.4 KiB (874.5 KiB/s) with 2 file(s) remaining \rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/674dc726261553b9bc253f92/contents/manifest.xml\nCompleted 102.0 KiB/141.4 KiB (874.5 KiB/s) with 1 file(s) remaining\rCompleted 141.4 KiB/141.4 KiB (1.1 MiB/s) with 1 file(s) remaining  \rupload: contents/Adlung2021 _model_jakstat_pa.sedml to s3://files.biosimulations.org/simulations/674dc726261553b9bc253f92/contents/Adlung2021 _model_jakstat_pa.sedml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.1 KiB/5.1 KiB (65.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc726261553b9bc253f92/rawLog.txt\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[1;33mProcess the metadata in the COMBINE archive ... failed due to: The metadata of the file could not be found:\nThere was an error in processing the metadata file. More information is available at https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/. A validation tool is available at https://run.biosimulations.org/utils/validate-metadata.\nPost the metadata to the API ... failed due to: Metadata not found due to a dependent step failing.\u001b[0m\n\u001b[0;31mPost the SED-ML file to the API ... failed due to: Failed to post SED-ML specs:\nThere was an error uploading the SED-ML specifications to the API.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":0.036584,"sedDocuments":[]}