{"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    451      0 --:--:-- --:--:-- --:--:--   451\r100   139  100   139    0     0    444      0 --:--:-- --:--:-- --:--:--   444\n\r100  5637  100  5637    0     0  13197      0 --:--:-- --:--:-- --:--:-- 13197\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\nThe 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 .\nsrun: error: xanadu-55: task 0: Exited with exit code 1\nsrun: Terminating job step 8798388.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 2.2 KiB/2.2 KiB (27.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 5.7 KiB/5.7 KiB (25.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/BIOMD0000000138_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000138_url.sedml/autogen_plot_for_task1.pdf (deflated 39%)\n  adding: outputs/reports.h5 (deflated 91%)\n  adding: rawLog.txt (deflated 68%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 26.1 KiB/26.1 KiB (79.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 5.8 KiB/22.1 KiB (48.3 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000138_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/outputs/BIOMD0000000138_url.sedml/autogen_plot_for_task1.pdf\nCompleted 5.8 KiB/22.1 KiB (48.3 KiB/s) with 3 file(s) remaining\rCompleted 9.4 KiB/22.1 KiB (73.7 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/rawLog.txt\nCompleted 9.4 KiB/22.1 KiB (73.7 KiB/s) with 2 file(s) remaining\rCompleted 18.6 KiB/22.1 KiB (79.4 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/output.zip\nCompleted 18.6 KiB/22.1 KiB (79.4 KiB/s) with 1 file(s) remaining\rCompleted 22.1 KiB/22.1 KiB (44.2 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/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/BIOMD0000000138_url.sedml  \n  inflating: contents/BIOMD0000000138_url.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 660 Bytes/42.9 KiB (5.4 KiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/contents/manifest.xml\nCompleted 660 Bytes/42.9 KiB (5.4 KiB/s) with 2 file(s) remaining\rCompleted 23.2 KiB/42.9 KiB (189.7 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000138_url.sedml to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/contents/BIOMD0000000138_url.sedml\nCompleted 23.2 KiB/42.9 KiB (189.7 KiB/s) with 1 file(s) remaining\rCompleted 42.9 KiB/42.9 KiB (167.6 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000138_url.xml to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/contents/BIOMD0000000138_url.xml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.8 KiB/5.8 KiB (36.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67868eaa1f52f47f628b665d/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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess 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.\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":1.104127,"sedDocuments":[{"location":"BIOMD0000000138_url.sedml","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  BIOMD0000000138_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 44 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_url.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_plot_for_task1`\r\n      `autogen_report_for_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[31mfailed\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `autogen_report_for_task1` ... \u001b[36mqueued\u001b[0m\r\n      Generating output 2: `autogen_plot_for_task1` ...","duration":0.658837,"tasks":[{"id":"task1","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[93mModel does not contain SBML fbc package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mModel does not contain SBML groups package\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'model_0000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n\u001b[93mWARNING:\u001b[0m \u001b[93mNo key provided for note in Model 'model_0000001'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n","duration":0.080916,"algorithm":null,"simulatorDetails":null}],"outputs":[{"id":"autogen_report_for_task1","status":"SKIPPED","exception":null,"skipReason":null,"output":"","duration":0.104774,"dataSets":[{"id":"autogen_time_for_task1","status":"SKIPPED"},{"id":"autogen_task1_c","status":"SKIPPED"},{"id":"autogen_task1_vca","status":"SKIPPED"},{"id":"autogen_task1_vk","status":"SKIPPED"},{"id":"autogen_task1_Cm","status":"SKIPPED"},{"id":"autogen_task1_gk","status":"SKIPPED"},{"id":"autogen_task1_gcal","status":"SKIPPED"},{"id":"autogen_task1_gsk","status":"SKIPPED"},{"id":"autogen_task1_ga","status":"SKIPPED"},{"id":"autogen_task1_gf","status":"SKIPPED"},{"id":"autogen_task1_vn","status":"SKIPPED"},{"id":"autogen_task1_va","status":"SKIPPED"},{"id":"autogen_task1_vm","status":"SKIPPED"},{"id":"autogen_task1_vh","status":"SKIPPED"},{"id":"autogen_task1_vf","status":"SKIPPED"},{"id":"autogen_task1_sn","status":"SKIPPED"},{"id":"autogen_task1_sa","status":"SKIPPED"},{"id":"autogen_task1_sm","status":"SKIPPED"},{"id":"autogen_task1_sh","status":"SKIPPED"},{"id":"autogen_task1_sf","status":"SKIPPED"},{"id":"autogen_task1_taun","status":"SKIPPED"},{"id":"autogen_task1_tauh","status":"SKIPPED"},{"id":"autogen_task1_lambda","status":"SKIPPED"},{"id":"autogen_task1_kc","status":"SKIPPED"},{"id":"autogen_task1_ks","status":"SKIPPED"},{"id":"autogen_task1_ff","status":"SKIPPED"},{"id":"autogen_task1_alpha","status":"SKIPPED"},{"id":"autogen_task1_phik","status":"SKIPPED"},{"id":"autogen_task1_phia","status":"SKIPPED"},{"id":"autogen_task1_phih","status":"SKIPPED"},{"id":"autogen_task1_phif","status":"SKIPPED"},{"id":"autogen_task1_phical","status":"SKIPPED"},{"id":"autogen_task1_cinf","status":"SKIPPED"},{"id":"autogen_task1_ica","status":"SKIPPED"},{"id":"autogen_task1_isk","status":"SKIPPED"},{"id":"autogen_task1_ibk","status":"SKIPPED"},{"id":"autogen_task1_ikdr","status":"SKIPPED"},{"id":"autogen_task1_ia","status":"SKIPPED"},{"id":"autogen_task1_ik","status":"SKIPPED"},{"id":"autogen_task1_n","status":"SKIPPED"},{"id":"autogen_task1_h","status":"SKIPPED"},{"id":"autogen_task1_V","status":"SKIPPED"},{"id":"autogen_task1_cell","status":"SKIPPED"},{"id":"autogen_task1_reaction_0000004","status":"SKIPPED"}]},{"id":"autogen_plot_for_task1","status":"SKIPPED","exception":null,"skipReason":null,"output":"","duration":0.301915,"curves":[{"id":"autogen_curve_task1_c","status":"SKIPPED"}]}]}]}