{"status":"SUCCEEDED","exception":null,"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    457      0 --:--:-- --:--:-- --:--:--   458\n\r100 14996  100 14996    0     0  36056      0 --:--:-- --:--:-- --:--:-- 36056\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 2\n      Skipped: 0\n      Failed: 0\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 1 SED documents:\n  SED documents (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Tasks (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Outputs (2):\n    Succeeded: 2\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (20.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 11.7 KiB/11.7 KiB (98.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 89%)\n  adding: outputs/reports.h5 (deflated 4%)\n  adding: outputs/BIOMD0000000407_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000407_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/1.0 MiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 512.0 KiB/1.0 MiB (2.6 MiB/s) with 1 file(s) remaining\rCompleted 768.0 KiB/1.0 MiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/1.0 MiB (1.4 MiB/s) with 1 file(s) remaining  \rCompleted 1.0 MiB/1.0 MiB (1.3 MiB/s) with 1 file(s) remaining  \rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 10.0 KiB/1.0 MiB (91.7 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/outputs/plots.zip\nCompleted 10.0 KiB/1.0 MiB (91.7 KiB/s) with 3 file(s) remaining\rCompleted 266.0 KiB/1.0 MiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 280.7 KiB/1.0 MiB (2.2 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000407_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/outputs/BIOMD0000000407_url.sedml/autogen_plot_for_task1.pdf\nCompleted 280.7 KiB/1.0 MiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 283.9 KiB/1.0 MiB (2.1 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/rawLog.txt\nCompleted 283.9 KiB/1.0 MiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 539.9 KiB/1.0 MiB (3.4 MiB/s) with 1 file(s) remaining\rCompleted 795.9 KiB/1.0 MiB (4.1 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/1.0 MiB (4.8 MiB/s) with 1 file(s) remaining  \rCompleted 1.0 MiB/1.0 MiB (3.1 MiB/s) with 1 file(s) remaining  \rupload: ./output.zip to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/output.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/BIOMD0000000407_url.sedml  \n  inflating: contents/BIOMD0000000407_url.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 77.3 KiB/198.2 KiB (662.5 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000407_url.sedml to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/contents/BIOMD0000000407_url.sedml\nCompleted 77.3 KiB/198.2 KiB (662.5 KiB/s) with 2 file(s) remaining\rCompleted 78.0 KiB/198.2 KiB (555.5 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/contents/manifest.xml\nCompleted 78.0 KiB/198.2 KiB (555.5 KiB/s) with 1 file(s) remaining\rCompleted 198.2 KiB/198.2 KiB (1.2 MiB/s) with 1 file(s) remaining \rupload: contents/BIOMD0000000407_url.xml to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/contents/BIOMD0000000407_url.xml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.6 KiB/5.6 KiB (53.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6752ecc89fa297efdca1ad80/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":2.791532,"sedDocuments":[{"location":"BIOMD0000000407_url.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  BIOMD0000000407_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 139 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 47 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000407_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 ...woohoo!\r\n \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_plot_for_task1` ...","duration":2.319772,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.403416,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"lsoda"},{"key":"parameters","value":null}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.696449,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_TNFR_E","status":"SUCCEEDED"},{"id":"autogen_task1_TNF_E","status":"SUCCEEDED"},{"id":"autogen_task1_TNF_TNFR_E","status":"SUCCEEDED"},{"id":"autogen_task1_TNFR","status":"SUCCEEDED"},{"id":"autogen_task1_RIP","status":"SUCCEEDED"},{"id":"autogen_task1_TRADD","status":"SUCCEEDED"},{"id":"autogen_task1_TRAF2","status":"SUCCEEDED"},{"id":"autogen_task1_FADD","status":"SUCCEEDED"},{"id":"autogen_task1_TNF_TNFR_TRADD","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRC1","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRCint1","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRCint2","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRCint3","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRC2","status":"SUCCEEDED"},{"id":"autogen_task1_FLIP","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRC2_FLIP","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRC2_pCasp8","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRC2_FLIP_FLIP","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRC2_pCasp8_pCasp8","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRC2_FLIP_pCasp8","status":"SUCCEEDED"},{"id":"autogen_task1_TNFRC2_FLIP_pCasp8_RIP_TRAF2","status":"SUCCEEDED"},{"id":"autogen_task1_IKK","status":"SUCCEEDED"},{"id":"autogen_task1_IKKa","status":"SUCCEEDED"},{"id":"autogen_task1_A20","status":"SUCCEEDED"},{"id":"autogen_task1_NFkB","status":"SUCCEEDED"},{"id":"autogen_task1_IkBa","status":"SUCCEEDED"},{"id":"autogen_task1_IkBa_NFkB","status":"SUCCEEDED"},{"id":"autogen_task1_PIkBa","status":"SUCCEEDED"},{"id":"autogen_task1_NFkB_N","status":"SUCCEEDED"},{"id":"autogen_task1_IkBa_N","status":"SUCCEEDED"},{"id":"autogen_task1_IkBa_NFkB_N","status":"SUCCEEDED"},{"id":"autogen_task1_A20_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_IkBa_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_XIAP_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_FLIP_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_BAR","status":"SUCCEEDED"},{"id":"autogen_task1_XIAP","status":"SUCCEEDED"},{"id":"autogen_task1_pCasp8","status":"SUCCEEDED"},{"id":"autogen_task1_pCasp3","status":"SUCCEEDED"},{"id":"autogen_task1_pCasp6","status":"SUCCEEDED"},{"id":"autogen_task1_Casp8","status":"SUCCEEDED"},{"id":"autogen_task1_Casp3","status":"SUCCEEDED"},{"id":"autogen_task1_Casp6","status":"SUCCEEDED"},{"id":"autogen_task1_BAR_Casp8","status":"SUCCEEDED"},{"id":"autogen_task1_XIAP_Casp3","status":"SUCCEEDED"},{"id":"autogen_task1_PARP","status":"SUCCEEDED"},{"id":"autogen_task1_cPARP","status":"SUCCEEDED"},{"id":"autogen_task1_cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_extracellular","status":"SUCCEEDED"},{"id":"autogen_task1_nucleus","status":"SUCCEEDED"},{"id":"autogen_task1_J1","status":"SUCCEEDED"},{"id":"autogen_task1_J2","status":"SUCCEEDED"},{"id":"autogen_task1_J3","status":"SUCCEEDED"},{"id":"autogen_task1_J4","status":"SUCCEEDED"},{"id":"autogen_task1_J5","status":"SUCCEEDED"},{"id":"autogen_task1_J6","status":"SUCCEEDED"},{"id":"autogen_task1_J7","status":"SUCCEEDED"},{"id":"autogen_task1_J8","status":"SUCCEEDED"},{"id":"autogen_task1_J9","status":"SUCCEEDED"},{"id":"autogen_task1_J10","status":"SUCCEEDED"},{"id":"autogen_task1_J11","status":"SUCCEEDED"},{"id":"autogen_task1_J12","status":"SUCCEEDED"},{"id":"autogen_task1_J13","status":"SUCCEEDED"},{"id":"autogen_task1_J14","status":"SUCCEEDED"},{"id":"autogen_task1_J15","status":"SUCCEEDED"},{"id":"autogen_task1_J16","status":"SUCCEEDED"},{"id":"autogen_task1_J17","status":"SUCCEEDED"},{"id":"autogen_task1_J18","status":"SUCCEEDED"},{"id":"autogen_task1_J19","status":"SUCCEEDED"},{"id":"autogen_task1_J20","status":"SUCCEEDED"},{"id":"autogen_task1_J21","status":"SUCCEEDED"},{"id":"autogen_task1_J22","status":"SUCCEEDED"},{"id":"autogen_task1_J23","status":"SUCCEEDED"},{"id":"autogen_task1_J24","status":"SUCCEEDED"},{"id":"autogen_task1_J25","status":"SUCCEEDED"},{"id":"autogen_task1_J26","status":"SUCCEEDED"},{"id":"autogen_task1_J27","status":"SUCCEEDED"},{"id":"autogen_task1_J28","status":"SUCCEEDED"},{"id":"autogen_task1_J29","status":"SUCCEEDED"},{"id":"autogen_task1_J30","status":"SUCCEEDED"},{"id":"autogen_task1_J31","status":"SUCCEEDED"},{"id":"autogen_task1_J32","status":"SUCCEEDED"},{"id":"autogen_task1_J33","status":"SUCCEEDED"},{"id":"autogen_task1_J34","status":"SUCCEEDED"},{"id":"autogen_task1_J35","status":"SUCCEEDED"},{"id":"autogen_task1_J36","status":"SUCCEEDED"},{"id":"autogen_task1_J37","status":"SUCCEEDED"},{"id":"autogen_task1_J38","status":"SUCCEEDED"},{"id":"autogen_task1_J39","status":"SUCCEEDED"},{"id":"autogen_task1_J40","status":"SUCC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