{"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    463      0 --:--:-- --:--:-- --:--:--   463\n\r100  2509  100  2509    0     0   6061      0 --:--:-- --:--:-- --:--:--  6061\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\u001b[31mNo module named 'libsbml'\u001b[0m\nsrun: error: xanadu-70: task 0: Exited with exit code 1\nsrun: Terminating job step 8544144.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 2.0 KiB/2.0 KiB (17.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6722486e2e0c0591a7c89429/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 154 Bytes/154 Bytes (2.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6722486e2e0c0591a7c89429/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 15%)\n  adding: rawLog.txt (deflated 69%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 1.4 KiB/4.4 KiB (17.0 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6722486e2e0c0591a7c89429/output.zip\nCompleted 1.4 KiB/4.4 KiB (17.0 KiB/s) with 1 file(s) remaining\rCompleted 4.4 KiB/4.4 KiB (37.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6722486e2e0c0591a7c89429/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/tmp605630      \n  inflating: contents/LEMS_NML2_Ex9_FN.sbml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 3.6 KiB/8.5 KiB (41.4 KiB/s) with 3 file(s) remaining\rupload: contents/LEMS_NML2_Ex9_FN.sbml to s3://files.biosimulations.org/simulations/6722486e2e0c0591a7c89429/contents/LEMS_NML2_Ex9_FN.sbml\nCompleted 3.6 KiB/8.5 KiB (41.4 KiB/s) with 2 file(s) remaining\rCompleted 4.2 KiB/8.5 KiB (41.6 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6722486e2e0c0591a7c89429/contents/manifest.xml\nCompleted 4.2 KiB/8.5 KiB (41.6 KiB/s) with 1 file(s) remaining\rCompleted 8.5 KiB/8.5 KiB (73.9 KiB/s) with 1 file(s) remaining\rupload: contents/tmp605630 to s3://files.biosimulations.org/simulations/6722486e2e0c0591a7c89429/contents/tmp605630\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 4.6 KiB/4.6 KiB (53.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6722486e2e0c0591a7c89429/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;32mRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess 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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... 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;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":0.02174,"sedDocuments":[]}