{"status":"FAILED","exception":{"type":"CombineArchiveExecutionError","message":"The COMBINE/OMEX did not execute successfully:\n\n  The SED document did not execute successfully:\n  \n    Could not load MassModel 'Adlung2021___Cell_to_cell_variability_in_JAK2_STAT5_pathway'\n  \n    target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='epo_level'] cannot be changed by XML manipulation, as the target is not an attribute of a model element"},"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    309      0 --:--:-- --:--:-- --:--:--   310\n\r  6  9542    6   606    0     0    818      0  0:00:11 --:--:--  0:00:11   818\r100  9542  100  9542    0     0  12781      0 --:--:-- --:--:-- --:--:-- 1454k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n \u001b[36mqueued\u001b[0m\n\n  Executed 2 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 0\n      Skipped: 0\n      Failed: 2\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 (2):\n    Succeeded: 0\n    Skipped: 0\n    Failed: 2\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    Could not load MassModel 'Adlung2021___Cell_to_cell_variability_in_JAK2_STAT5_pathway'\n  \n    target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='epo_level'] cannot be changed by XML manipulation, as the target is not an attribute of a model element\nsrun: error: xanadu-55: task 0: Exited with exit code 1\nsrun: Terminating job step 8798443.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 2.1 KiB/2.1 KiB (11.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 7.4 KiB/7.4 KiB (38.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/Adlung2021 _model_jakstat_pa.sedml/ (stored 0%)\n  adding: outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.pdf (deflated 39%)\n  adding: outputs/reports.h5 (deflated 91%)\n  adding: rawLog.txt (deflated 66%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 53.0 KiB/53.0 KiB (571.5 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 11.5 KiB/24.3 KiB (141.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/output.zip\nCompleted 11.5 KiB/24.3 KiB (141.2 KiB/s) with 3 file(s) remaining\rCompleted 15.1 KiB/24.3 KiB (151.3 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/outputs/plots.zip\nCompleted 15.1 KiB/24.3 KiB (151.3 KiB/s) with 2 file(s) remaining\rCompleted 20.9 KiB/24.3 KiB (160.2 KiB/s) with 2 file(s) remaining\rupload: outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.pdf to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.pdf\nCompleted 20.9 KiB/24.3 KiB (160.2 KiB/s) with 1 file(s) remaining\rCompleted 24.3 KiB/24.3 KiB (60.7 KiB/s) with 1 file(s) remaining \rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/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 678 Bytes/141.4 KiB (5.5 KiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/contents/manifest.xml\nCompleted 678 Bytes/141.4 KiB (5.5 KiB/s) with 2 file(s) remaining\rCompleted 102.0 KiB/141.4 KiB (738.7 KiB/s) with 2 file(s) remaining\rupload: contents/Adlung2021 _model_jakstat_pa.xml to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/contents/Adlung2021 _model_jakstat_pa.xml\nCompleted 102.0 KiB/141.4 KiB (738.7 KiB/s) with 1 file(s) remaining\rCompleted 141.4 KiB/141.4 KiB (622.1 KiB/s) with 1 file(s) remaining\rupload: contents/Adlung2021 _model_jakstat_pa.sedml to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/contents/Adlung2021 _model_jakstat_pa.sedml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.7 KiB/5.7 KiB (67.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67869098ba5a3f02b9f3036b/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 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.\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":1.815116,"sedDocuments":[{"location":"Adlung2021 _model_jakstat_pa.sedml","status":"FAILED","exception":{"type":"SedmlExecutionError","message":"The SED document did not execute successfully:\n\n  Could not load MassModel 'Adlung2021___Cell_to_cell_variability_in_JAK2_STAT5_pathway'\n\n  target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='epo_level'] cannot be changed by XML manipulation, as the target is not an attribute of a model element"},"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 1 plots:\r\n  Adlung2021 _model_jakstat_pa.sedml:\r\n    Tasks (2):\r\n      task1\r\n      task2\r\n    Reports (1):\r\n      autogen_report_for_task2: 71 data sets\r\n    Plots (1):\r\n      plot_2_task2: 2 curves\r\n\r\nExecuting SED-ML file 1: Adlung2021 _model_jakstat_pa.sedml ...\r\n  Found 2 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n      `task2`\r\n    Outputs:\r\n      `autogen_report_for_task2`\r\n      `plot_2_task2`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[31mfailed\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `plot_2_task2` ... \u001b[36mqueued\u001b[0m\r\n      Generating output 2: `autogen_report_for_task2` ... \u001b[36mqueued\u001b[0m\r\n  Executing task 2: `task2`\r\n    Executing simulation ... \u001b[31mfailed\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `plot_2_task2` ... \u001b[36mqueued\u001b[0m\r\n      Generating output 2: `autogen_report_for_task2` ...","duration":1.253725,"tasks":[{"id":"task1","status":"FAILED","exception":{"type":"MassSimulationError","message":"Could not load MassModel 'Adlung2021___Cell_to_cell_variability_in_JAK2_STAT5_pathway'"},"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 'Adlung2021___Cell_to_cell_variability_in_JAK2_STAT5_pathway'. The note will be added to the notes attribute with key 'NOTES'.\u001b[0m\r\n","duration":0.333169,"algorithm":null,"simulatorDetails":null},{"id":"task2","status":"FAILED","exception":{"type":"NotImplementedError","message":"target /sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@id='epo_level'] cannot be changed by XML manipulation, as the target is not an attribute of a model element"},"skipReason":null,"output":"","duration":0.03937,"algorithm":null,"simulatorDetails":null}],"outputs":[{"id":"plot_2_task2","status":"SKIPPED","exception":null,"skipReason":null,"output":"","duration":0.110868,"curves":[{"id":"p1_curve_1_task2","status":"SKIPPED"},{"id":"p1_curve_2_task2","status":"SKIPPED"}]},{"id":"autogen_report_for_task2","status":"SKIPPED","exception":null,"skipReason":null,"output":"","duration":0.075259,"dataSets":[{"id":"autogen_time_for_task2","status":"SKIPPED"},{"id":"autogen_task2_measuralbe_pSTAT5","status":"SKIPPED"},{"id":"autogen_task2__pSTAT5_Total_STAT5","status":"SKIPPED"},{"id":"autogen_task2_EpoRJAK2","status":"SKIPPED"},{"id":"autogen_task2_EpoRpJAK2","status":"SKIPPED"},{"id":"autogen_task2_p1EpoRpJAK2","status":"SKIPPED"},{"id":"autogen_task2_p2EpoRpJAK2","status":"SKIPPED"},{"id":"autogen_task2_p12EpoRpJAK2","status":"SKIPPED"},{"id":"autogen_task2_SHP1","status":"SKIPPED"},{"id":"autogen_task2_SHP1Act","status":"SKIPPED"},{"id":"autogen_task2_STAT5","status":"SKIPPED"},{"id":"autogen_task2_pSTAT5","status":"SKIPPED"},{"id":"autogen_task2_npSTAT5","status":"SKIPPED"},{"id":"autogen_task2_CISnRNA1","status":"SKIPPED"},{"id":"autogen_task2_CISnRNA2","status":"SKIPPED"},{"id":"autogen_task2_CISRNA","status":"SKIPPED"},{"id":"autogen_task2_CIS","status":"SKIPPED"},{"id":"autogen_task2_SOCS3","status":"SKIPPED"},{"id":"autogen_task2_ActD","status":"SKIPPED"},{"id":"autogen_task2_CISEqc","status":"SKIPPED"},{"id":"autogen_task2_CISInh","status":"SKIPPED"},{"id":"autogen_task2_CISRNADelay","status":"SKIPPED"},{"id":"autogen_task2_CISRNAEqc","status":"SKIPPED"},{"id":"autogen_task2_CISRNATurn","status":"SKIPPED"},{"id":"autogen_task2_CISTurn","status":"SKIPPED"},{"id":"autogen_task2_DeaEpoRJAKActSHP1","status":"SKIPPED"},{"id":"autogen_task2_EpoRActJAK2","status":"SKIPPED"},{"id":"autogen_task2_JAK2ActEpo","status":"SKIPPED"},{"id":"autogen_task2_SHP1ActEpoR","status":"SKIPPED"},{"id":"autogen_task2_SHP1Dea","status":"SKIPPED"},{"id":"autogen_task2_SOCS3Eqc","status":"SKIPPED"},{"id":"autogen_task2_SOCS3EqcOE","status":"SKIPPED"},{"id":"autogen_task2_SOCS3Inh","status":"SKIPPED"},{"id":"autogen_task2_SOCS3Turn","status":"SKIPPED"},{"id":"autogen_task2_SOCS3oe","status":"SKIPPED"},{"id":"autogen_task2_STAT5ActEpoR","status":"SKIPPED"},{"id":"autogen_task2_STAT5ActJAK2","status":"SKIPPED"},{"id":"autogen_task2_STAT5Exp","status":"SKIPPED"},{"id":"autogen_task2_STAT5Imp","status":"SKIPPED"},{"id":"autogen_task2_epo_level","status":"SKIPPED"},{"id":"autogen_task2_init_EpoRJAK2","status":"SKIPPED"},{"id":"autogen_task2_init_SHP1","status":"SKIPPED"},{"id":"autogen_task2_init_STAT5","status":"SKIPPED"},{"id":"autogen_task2_Epo","status":"SKIPPED"},{"id":"autogen_task2_Total_STAT5","status":"SKIPPED"},{"id":"autogen_task2_cyt","status":"SKIPPED"},{"id":"autogen_task2_nuc","status":"SKIPPED"},{"id":"autogen_task2_v1_v_0","status":"SKIPPED"},{"id":"autogen_task2_v2_v_1","status":"SKIPPED"},{"id":"autogen_task2_v3_v_2","status":"SKIPPED"},{"id":"autogen_task2_v4_v_3","status":"SKIPPED"},{"id":"autogen_task2_v5_v_4","status":"SKIPPED"},{"id":"autogen_task2_v6_v_5","status":"SKIPPED"},{"id":"autogen_task2_v7_v_6","status":"SKIPPED"},{"id":"autogen_task2_v8_v_7","status":"SKIPPED"},{"id":"autogen_task2_v9_v_8","status":"SKIPPED"},{"id":"autogen_task2_v12_v_11","status":"SKIPPED"},{"id":"autogen_task2_v13_v_12","status":"SKIPPED"},{"id":"autogen_task2_v14_v_13","status":"SKIPPED"},{"id":"autogen_task2_v15_v_14","status":"SKIPPED"},{"id":"autogen_task2_v16_v_15","status":"SKIPPED"},{"id":"autogen_task2_v17_v_16","status":"SKIPPED"},{"id":"autogen_task2_v18_v_17","status":"SKIPPED"},{"id":"autogen_task2_v19_v_18","status":"SKIPPED"},{"id":"autogen_task2_v20_v_19","status":"SKIPPED"},{"id":"autogen_task2_v21_v_20","status":"SKIPPED"},{"id":"autogen_task2_v22_v_21","status":"SKIPPED"},{"id":"autogen_task2_v23_v_22","status":"SKIPPED"},{"id":"autogen_task2_v24_v_23","status":"SKIPPED"},{"id":"autogen_task2_v25_v_24","status":"SKIPPED"},{"id":"autogen_task2_v26_v_25","status":"SKIPPED"}]}]}]}