{"status":"FAILED","exception":{"type":"ValueError","message":"`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n  - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n    - Simulation `sim1` is invalid.\n      - Algorithm has an invalid KiSAO id `KISAO_0000694`."},"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    468      0 --:--:-- --:--:-- --:--:--   468\n\r100  9542  100  9542    0     0  22420      0 --:--:-- --:--:-- --:--:-- 22420\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n\r\nINFO: No xlwt module available, Excel spreadsheet creation disabled\r\n\r\n\r\n\r\nNo module named 'cplex'\r\n\r\n\r\n\r\nCPLEX not available\r\n\r\n*****\r\nUsing GLPK\r\n*****\r\n\r\n\r\nINFO: No xlrd module available, Excel spreadsheet reading disabled\r\n\r\nCBMPy environment\r\n******************\r\nRevision: r689\r\n\r\n\r\n***********************************************************************\r\n* Welcome to CBMPy (0.7.25) - PySCeS Constraint Based Modelling       *\r\n*                http://cbmpy.sourceforge.net                         *\r\n* Copyright(C) Brett G. Olivier 2014 - 2019                           *\r\n* Dept. of Systems Bioinformatics                                     *\r\n* Vrije Universiteit Amsterdam, Amsterdam, The Netherlands            *\r\n* CBMPy is developed as part of the BeBasic MetaToolKit Project       *\r\n* Distributed under the GNU GPL v 3.0 licence, see                    *\r\n* LICENCE (supplied with this release) for details                    *\r\n***********************************************************************\r\n\r\n\u001b[31m`/root/archive.omex` is not a valid COMBINE/OMEX archive.\n  - The SED-ML file at location `./Adlung2021 _model_jakstat_pa.sedml` is invalid.\n    - Simulation `sim1` is invalid.\n      - Algorithm has an invalid KiSAO id `KISAO_0000694`.\u001b[0m\nsrun: error: xanadu-55: task 0: Exited with exit code 1\nsrun: Terminating job step 8798437.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 2.5 KiB/2.5 KiB (14.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6786908bba5a3f02b9f3035a/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 1.5 KiB/1.5 KiB (8.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6786908bba5a3f02b9f3035a/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 53%)\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 2.2 KiB/5.7 KiB (19.8 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6786908bba5a3f02b9f3035a/output.zip\nCompleted 2.2 KiB/5.7 KiB (19.8 KiB/s) with 1 file(s) remaining\rCompleted 5.7 KiB/5.7 KiB (46.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6786908bba5a3f02b9f3035a/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/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 (912.2 KiB/s) with 3 file(s) remaining\rupload: contents/Adlung2021 _model_jakstat_pa.xml to s3://files.biosimulations.org/simulations/6786908bba5a3f02b9f3035a/contents/Adlung2021 _model_jakstat_pa.xml\nCompleted 101.3 KiB/141.4 KiB (912.2 KiB/s) with 2 file(s) remaining\rCompleted 102.0 KiB/141.4 KiB (893.9 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6786908bba5a3f02b9f3035a/contents/manifest.xml\nCompleted 102.0 KiB/141.4 KiB (893.9 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/6786908bba5a3f02b9f3035a/contents/Adlung2021 _model_jakstat_pa.sedml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.2 KiB/5.2 KiB (58.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6786908bba5a3f02b9f3035a/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 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":0.300109,"sedDocuments":[]}