{"status":"FAILED","exception":{"type":"CombineArchiveExecutionError","message":"The COMBINE/OMEX did not execute successfully:\n\n  The SED document did not execute successfully:\n  \n    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n    \t`(model, errors) = validate_sbml_model(filename)`\n    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues ."},"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    459      0 --:--:-- --:--:-- --:--:--   460\n\r 24  2509   24   603    0     0   1399      0  0:00:01 --:--:--  0:00:01  1399\r100  2509  100  2509    0     0   5757      0 --:--:-- --:--:-- --:--:--  465k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n \u001b[36mqueued\u001b[0m\n\n  Executed 1 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 0\n      Skipped: 0\n      Failed: 1\n    Outputs:\n      Succeeded: 0\n      Skipped: 2\n      Failed: 0\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 1 SED documents:\n  SED documents (1):\n    Succeeded: 0\n    Skipped: 0\n    Failed: 1\n  Tasks (1):\n    Succeeded: 0\n    Skipped: 0\n    Failed: 1\n  Outputs (2):\n    Succeeded: 0\n    Skipped: 2\n    Failed: 0\n\n\u001b[31mThe COMBINE/OMEX did not execute successfully:\n\n  The SED document did not execute successfully:\n  \n    Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n    \t`(model, errors) = validate_sbml_model(filename)`\n    If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues .\u001b[0m\nsrun: error: xanadu-74: task 0: Exited with exit code 1\nsrun: Terminating job step 8537566.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 2.2 KiB/2.2 KiB (26.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 3.2 KiB/3.2 KiB (36.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 69%)\n  adding: outputs/tmp324745/ (stored 0%)\n  adding: outputs/tmp324745/d1.pdf (deflated 39%)\n  adding: outputs/reports.h5 (deflated 96%)\n  adding: rawLog.txt (deflated 67%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 22.8 KiB/22.8 KiB (280.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 7.5 KiB/20.2 KiB (90.0 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/output.zip\nCompleted 7.5 KiB/20.2 KiB (90.0 KiB/s) with 3 file(s) remaining\rCompleted 13.3 KiB/20.2 KiB (117.3 KiB/s) with 3 file(s) remaining\rupload: outputs/tmp324745/d1.pdf to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/outputs/tmp324745/d1.pdf\nCompleted 13.3 KiB/20.2 KiB (117.3 KiB/s) with 2 file(s) remaining\rCompleted 16.8 KiB/20.2 KiB (130.8 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/rawLog.txt\nCompleted 16.8 KiB/20.2 KiB (130.8 KiB/s) with 1 file(s) remaining\rCompleted 20.2 KiB/20.2 KiB (144.9 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/outputs/plots.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/tmp324745      \n  inflating: contents/LEMS_NML2_Ex9_FN.sbml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 642 Bytes/8.5 KiB (7.2 KiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/contents/manifest.xml\nCompleted 642 Bytes/8.5 KiB (7.2 KiB/s) with 2 file(s) remaining\rCompleted 4.9 KiB/8.5 KiB (44.7 KiB/s) with 2 file(s) remaining \rupload: contents/tmp324745 to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/contents/tmp324745\nCompleted 4.9 KiB/8.5 KiB (44.7 KiB/s) with 1 file(s) remaining\rCompleted 8.5 KiB/8.5 KiB (75.0 KiB/s) with 1 file(s) remaining\rupload: contents/LEMS_NML2_Ex9_FN.sbml to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/contents/LEMS_NML2_Ex9_FN.sbml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.6 KiB/5.6 KiB (71.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/671f7f5e953bc3bf105eaaf4/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.\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":0.584422,"sedDocuments":[{"location":"tmp324745","status":"FAILED","exception":{"type":"SedmlExecutionError","message":"The SED document did not execute successfully:\n\n  Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n  \t`(model, errors) = validate_sbml_model(filename)`\n  If the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues ."},"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  tmp324745:\r\n    Tasks (1):\r\n      sim1_net1\r\n    Reports (1):\r\n      ex9: 3 data sets\r\n    Plots (1):\r\n      d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp324745 ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `sim1_net1`\r\n    Outputs:\r\n      `d1`\r\n      `ex9`\r\n  Executing task 1: `sim1_net1`\r\n    Executing simulation ... \u001b[31mfailed\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n      Generating output 2: `ex9` ...","duration":0.346074,"tasks":[{"id":"sim1_net1","status":"FAILED","exception":{"type":"MassSBMLError","message":"Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the `mass.io.sbml.validate_sbml_model` function or via the online validator at http://sbml.org/validator .\n\t`(model, errors) = validate_sbml_model(filename)`\nIf the model is valid and cannot be read please open an issue at https://github.com/SBRG/masspy/issues ."},"skipReason":null,"output":"\u001b[93mWARNING:\u001b[0m \u001b[93mSBML model is written as Level 2 Version 2, will attempt to convert the SBML model from Level 2 Version 2 to Level 3 Version 1 before parsing\u001b[0m\r\n","duration":0.039226,"algorithm":null,"simulatorDetails":null}],"outputs":[{"id":"d1","status":"SKIPPED","exception":null,"skipReason":null,"output":"","duration":0.148526,"curves":[{"id":"curve_V","status":"SKIPPED"},{"id":"curve_W","status":"SKIPPED"}]},{"id":"ex9","status":"SKIPPED","exception":null,"skipReason":null,"output":"","duration":0.068371,"dataSets":[{"id":"ex9_time","status":"SKIPPED"},{"id":"ex9_V","status":"SKIPPED"},{"id":"ex9_W","status":"SKIPPED"}]}]}]}