{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    458      0 --:--:-- --:--:-- --:--:--   458\n\r100 13790  100 13790    0     0  30701      0 --:--:-- --:--:-- --:--:-- 30701\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/tmpmn01a13j/./Theinmozhi_2018.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 8658212.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 2.5 KiB/2.5 KiB (31.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc667ef911d5d45259ae3/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 571 Bytes/571 Bytes (4.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/674dc667ef911d5d45259ae3/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 67%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 1.9 KiB/5.3 KiB (15.2 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/674dc667ef911d5d45259ae3/output.zip\nCompleted 1.9 KiB/5.3 KiB (15.2 KiB/s) with 1 file(s) remaining\rCompleted 5.3 KiB/5.3 KiB (41.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc667ef911d5d45259ae3/rawLog.txt\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/manifest.xml   \n  inflating: contents/Theinmozhi_2018.sedml  \n  inflating: contents/Theinmozhi_2018.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 185.5 KiB/252.4 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/Theinmozhi_2018.xml to s3://files.biosimulations.org/simulations/674dc667ef911d5d45259ae3/contents/Theinmozhi_2018.xml\nCompleted 185.5 KiB/252.4 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 186.1 KiB/252.4 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/674dc667ef911d5d45259ae3/contents/manifest.xml\nCompleted 186.1 KiB/252.4 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 252.4 KiB/252.4 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/Theinmozhi_2018.sedml to s3://files.biosimulations.org/simulations/674dc667ef911d5d45259ae3/contents/Theinmozhi_2018.sedml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.1 KiB/5.1 KiB (50.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc667ef911d5d45259ae3/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.\nProcess and upload the outputs of the simulation run ... 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.\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":0.070162,"sedDocuments":[]}