{"status":"FAILED","exception":{"type":"ValueError","message":"`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n  - The SED-ML file at location `./tmp20997` is invalid.\n    - Data generator `OBJF_1` is invalid.\n      - Variable `OBJF` is invalid.\n        - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`."},"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    468      0 --:--:-- --:--:-- --:--:--   469\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  3841  100  3841    0     0   9325      0 --:--:-- --:--:-- --:--:-- 36932\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\nlibtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified                          in the user configuration file, set \"matplotlib_backend = <backend>\" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems   *\r\n*                http://pysces.sourceforge.net                        *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024  *\r\n* Triple-J Group for Molecular Cell Physiology                        *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL         *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see     *\r\n* LICENCE.txt (supplied with this release) for details                *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046          *\r\n***********************************************************************\r\n`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n  - The SED-ML file at location `./tmp20997` is invalid.\n    - Data generator `OBJF_1` is invalid.\n      - Variable `OBJF` is invalid.\n        - One or more namespaces required for target `/sbml:sbml/sbml:model/fbc:listOfObjectives/fbc:objective[@fbc:id='OBJF']` are not defined. Only the following namespaces are defined for the target: `sbml`.\nsrun: error: xanadu-62: task 0: Exited with exit code 1\nsrun: Terminating job step 8598529.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 3.0 KiB/3.0 KiB (34.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6734b85c5a60072d20f59f76/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 2.0 KiB/2.0 KiB (23.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6734b85c5a60072d20f59f76/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 51%)\n  adding: rawLog.txt (deflated 62%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 2.8 KiB/6.7 KiB (35.7 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6734b85c5a60072d20f59f76/output.zip\nCompleted 2.8 KiB/6.7 KiB (35.7 KiB/s) with 1 file(s) remaining\rCompleted 6.7 KiB/6.7 KiB (55.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6734b85c5a60072d20f59f76/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/tmp20997       \n  inflating: contents/01186-sbml-l3v2.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 32.5 KiB/35.2 KiB (334.8 KiB/s) with 3 file(s) remaining\rupload: contents/01186-sbml-l3v2.xml to s3://files.biosimulations.org/simulations/6734b85c5a60072d20f59f76/contents/01186-sbml-l3v2.xml\nCompleted 32.5 KiB/35.2 KiB (334.8 KiB/s) with 2 file(s) remaining\rCompleted 33.1 KiB/35.2 KiB (306.6 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6734b85c5a60072d20f59f76/contents/manifest.xml\nCompleted 33.1 KiB/35.2 KiB (306.6 KiB/s) with 1 file(s) remaining\rCompleted 35.2 KiB/35.2 KiB (292.5 KiB/s) with 1 file(s) remaining\rupload: contents/tmp20997 to s3://files.biosimulations.org/simulations/6734b85c5a60072d20f59f76/contents/tmp20997\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.5 KiB/5.5 KiB (66.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6734b85c5a60072d20f59f76/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 and upload the outputs of the simulation run ... 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 the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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":0.212339,"sedDocuments":[]}