{"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    453      0 --:--:-- --:--:-- --:--:--   454\n\r100 27761  100 27761    0     0  66912      0 --:--:-- --:--:-- --:--:-- 66912\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 (24.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/rawLog.txt\nCompleted 5.4 KiB/5.4 KiB (90.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/Stucki2005.sedml/ (stored 0%)\n  adding: outputs/Stucki2005.sedml/plot_1_task1.pdf (deflated 27%)\n  adding: outputs/reports.h5 (deflated 16%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 194.8 KiB/194.8 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/outputs/reports.h5\nCompleted 176.2 KiB/201.3 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/output.zip\nCompleted 176.2 KiB/201.3 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 189.4 KiB/201.3 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: outputs/Stucki2005.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/outputs/Stucki2005.sedml/plot_1_task1.pdf\nCompleted 189.4 KiB/201.3 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 198.7 KiB/201.3 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/outputs/plots.zip\nCompleted 198.7 KiB/201.3 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 201.3 KiB/201.3 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Stucki2005-biopax2.owl  \n  inflating: contents/Stucki2005-biopax3.owl  \n  inflating: contents/Stucki2005-matlab.m  \n  inflating: contents/Stucki2005-octave.m  \n  inflating: contents/Stucki2005.cps  \n  inflating: contents/Stucki2005.sedml  \n  inflating: contents/Stucki2005.xml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 46.1 KiB/313.7 KiB (601.8 KiB/s) with 9 file(s) remaining\rupload: contents/Stucki2005-biopax3.owl to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/contents/Stucki2005-biopax3.owl\nCompleted 46.1 KiB/313.7 KiB (601.8 KiB/s) with 8 file(s) remaining\rCompleted 56.0 KiB/313.7 KiB (510.6 KiB/s) with 8 file(s) remaining\rupload: contents/Stucki2005-octave.m to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/contents/Stucki2005-octave.m\nCompleted 56.0 KiB/313.7 KiB (510.6 KiB/s) with 7 file(s) remaining\rCompleted 65.8 KiB/313.7 KiB (594.2 KiB/s) with 7 file(s) remaining\rupload: contents/Stucki2005-matlab.m to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/contents/Stucki2005-matlab.m\nCompleted 65.8 KiB/313.7 KiB (594.2 KiB/s) with 6 file(s) remaining\rCompleted 93.6 KiB/313.7 KiB (816.3 KiB/s) with 6 file(s) remaining\rupload: contents/Stucki2005-biopax2.owl to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/contents/Stucki2005-biopax2.owl\nCompleted 93.6 KiB/313.7 KiB (816.3 KiB/s) with 5 file(s) remaining\rCompleted 94.8 KiB/313.7 KiB (797.3 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/contents/metadata.rdf\nCompleted 94.8 KiB/313.7 KiB (797.3 KiB/s) with 4 file(s) remaining\rCompleted 127.8 KiB/313.7 KiB (935.9 KiB/s) with 4 file(s) remaining\rupload: contents/Stucki2005.sedml to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/contents/Stucki2005.sedml\nCompleted 127.8 KiB/313.7 KiB (935.9 KiB/s) with 3 file(s) remaining\rCompleted 212.3 KiB/313.7 KiB (1.4 MiB/s) with 3 file(s) remaining  \rupload: contents/Stucki2005.xml to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/contents/Stucki2005.xml\nCompleted 212.3 KiB/313.7 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 213.3 KiB/313.7 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/contents/manifest.xml\nCompleted 213.3 KiB/313.7 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 313.7 KiB/313.7 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/Stucki2005.cps to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/contents/Stucki2005.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 6.4 KiB/6.4 KiB (84.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f187da4ff2037f59c2e5/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Stucki2005.sedml\ncreating dataset /Stucki2005.sedml/autogen_report_for_task1, shape: (56, 1001), type: float64\ndataset created, uuid: d-ae01712c-91361922-6a59-0d9689-afaa1f, chunk_size: (56, 1001)\ncreating dataset /Stucki2005.sedml/plot_1_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-ae01712c-91361922-3294-f2a795-97d0fe, chunk_size: (9, 1001)\ncreating attribute combineArchiveLocation in /Stucki2005.sedml\ncreating attribute uri in /Stucki2005.sedml\ncreating attribute _type in /Stucki2005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Stucki2005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Stucki2005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Stucki2005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Stucki2005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Stucki2005.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Stucki2005.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Stucki2005.sedml/autogen_report_for_task1\ncreating attribute uri in /Stucki2005.sedml/autogen_report_for_task1\ncreating attribute _type in /Stucki2005.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Stucki2005.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Stucki2005.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Stucki2005.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Stucki2005.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Stucki2005.sedml/plot_1_task1\ncreating attribute sedmlId in /Stucki2005.sedml/plot_1_task1\ncreating attribute sedmlName in /Stucki2005.sedml/plot_1_task1\ncreating attribute uri in /Stucki2005.sedml/plot_1_task1\ncreate_links: /\ngot link: Stucki2005.sedml\ncreate_links: /Stucki2005.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Stucki2005.sedml/autogen_report_for_task1 to tgt: /Stucki2005.sedml/autogen_report_for_task1, shape: (56, 1001), type: float64\niterating over chunks for /Stucki2005.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 56, 1), slice(0, 1001, 1))\ndone with dataload for /Stucki2005.sedml/autogen_report_for_task1\nwrite_dataset src: /Stucki2005.sedml/plot_1_task1 to tgt: /Stucki2005.sedml/plot_1_task1, shape: (9, 1001), type: float64\niterating over chunks for /Stucki2005.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /Stucki2005.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f187da4ff2037f59c2e5\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... 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.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.59121,"sedDocuments":[{"location":"Stucki2005.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  Stucki2005.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 56 data sets\r\n    Plots (1):\r\n      plot_1_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: Stucki2005.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":1.189966,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.188881,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":100000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.442042,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"},{"id":"p1_curve_4_task1","status":"SUCCEEDED"},{"id":"p1_curve_5_task1","status":"SUCCEEDED"},{"id":"p1_curve_6_task1","status":"SUCCEEDED"},{"id":"p1_curve_7_task1","status":"SUCCEEDED"},{"id":"p1_curve_8_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.393296,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_c3","status":"SUCCEEDED"},{"id":"autogen_task1_iap","status":"SUCCEEDED"},{"id":"autogen_task1_survivin","status":"SUCCEEDED"},{"id":"autogen_task1_cascade","status":"SUCCEEDED"},{"id":"autogen_task1_iapc3","status":"SUCCEEDED"},{"id":"autogen_task1_iapsmac","status":"SUCCEEDED"},{"id":"autogen_task1_sursmac","status":"SUCCEEDED"},{"id":"autogen_task1_smac","status":"SUCCEEDED"},{"id":"autogen_task1_pc3","status":"SUCCEEDED"},{"id":"autogen_task1_smacmit","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_km5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_km6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k8","status":"SUCCEEDED"},{"id":"autogen_task1_km8","status":"SUCCEEDED"},{"id":"autogen_task1_k9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_k11","status":"SUCCEEDED"},{"id":"autogen_task1_k12","status":"SUCCEEDED"},{"id":"autogen_task1_k13","status":"SUCCEEDED"},{"id":"autogen_task1_k14","status":"SUCCEEDED"},{"id":"autogen_task1_k15","status":"SUCCEEDED"},{"id":"autogen_task1_k16","status":"SUCCEEDED"},{"id":"autogen_task1_k17","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_H","status":"SUCCEEDED"},{"id":"autogen_task1_k10_cascade","status":"SUCCEEDED"},{"id":"autogen_task1_Cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_procaspase_3","status":"SUCCEEDED"},{"id":"autogen_task1_cleavage_of_procaspase_3_into_caspase_3","status":"SUCCEEDED"},{"id":"autogen_task1_caspase_3_proteolysis","status":"SUCCEEDED"},{"id":"autogen_task1_IAP_caspas_3_complex_formation","status":"SUCCEEDED"},{"id":"autogen_task1_Separation_of_caspase_3_and_iap","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_caspas_3","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_iap_smac_complex","status":"SUCCEEDED"},{"id":"autogen_task1_Separation_of_iap_and_smac","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_iap","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_iap","status":"SUCCEEDED"},{"id":"autogen_task1_release_of_smac_in_cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_smac_survivin_complex","status":"SUCCEEDED"},{"id":"autogen_task1_cleavage_of_smac_survivin_complex","status":"SUCCEEDED"},{"id":"autogen_task1_Productio_of_survivin","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_survivin","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_iap_caspase_3_complex","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_iapsmac","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_sursmac","status":"SUCCEEDED"},{"id":"autogen_task1_activation_of_cascade_controled_by_caspase_3","status":"SUCCEEDED"},{"id":"autogen_task1_Auto_amplification_of_cascade","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_cascade","status":"SUCCEEDED"}]}]}]}