{"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 52939  100 52939    0     0   125k      0 --:--:-- --:--:-- --:--:--  125k\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 (22.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (67.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/Cappuccio2006 v9.0.sedml/ (stored 0%)\n  adding: outputs/Cappuccio2006 v9.0.sedml/plot_1_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 57%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 44.8 KiB/44.8 KiB (448.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/outputs/reports.h5\nCompleted 28.5 KiB/47.5 KiB (412.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/output.zip\nCompleted 28.5 KiB/47.5 KiB (412.3 KiB/s) with 3 file(s) remaining\rCompleted 35.1 KiB/47.5 KiB (329.6 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/outputs/plots.zip\nCompleted 35.1 KiB/47.5 KiB (329.6 KiB/s) with 2 file(s) remaining\rCompleted 44.9 KiB/47.5 KiB (409.6 KiB/s) with 2 file(s) remaining\rupload: outputs/Cappuccio2006 v9.0.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/outputs/Cappuccio2006 v9.0.sedml/plot_1_task1.pdf\nCompleted 44.9 KiB/47.5 KiB (409.6 KiB/s) with 1 file(s) remaining\rCompleted 47.5 KiB/47.5 KiB (363.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Cappuccio2006 v2.0-biopax2.owl  \n  inflating: contents/Cappuccio2006 v2.0-biopax3.owl  \n  inflating: contents/Cappuccio2006 v2.0-matlab.m  \n  inflating: contents/Cappuccio2006 v2.0-octave.m  \n  inflating: contents/Cappuccio2006 v2.0.ode  \n  inflating: contents/Cappuccio2006 v2.0.xml  \n  inflating: contents/Cappuccio2006 v9.0.cps  \n  inflating: contents/Cappuccio2006 v9.0.sedml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 18.4 KiB/286.8 KiB (248.6 KiB/s) with 12 file(s) remaining\rupload: contents/Cappuccio2006 v2.0-biopax2.owl to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/Cappuccio2006 v2.0-biopax2.owl\nCompleted 18.4 KiB/286.8 KiB (248.6 KiB/s) with 11 file(s) remaining\rCompleted 26.6 KiB/286.8 KiB (239.2 KiB/s) with 11 file(s) remaining\rupload: contents/Cappuccio2006 v2.0-matlab.m to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/Cappuccio2006 v2.0-matlab.m\nCompleted 26.6 KiB/286.8 KiB (239.2 KiB/s) with 10 file(s) remaining\rCompleted 34.7 KiB/286.8 KiB (304.1 KiB/s) with 10 file(s) remaining\rupload: contents/Cappuccio2006 v2.0-octave.m to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/Cappuccio2006 v2.0-octave.m\nCompleted 34.7 KiB/286.8 KiB (304.1 KiB/s) with 9 file(s) remaining\rCompleted 40.6 KiB/286.8 KiB (316.9 KiB/s) with 9 file(s) remaining\rupload: contents/Cappuccio2006 v2.0.ode to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/Cappuccio2006 v2.0.ode\nCompleted 40.6 KiB/286.8 KiB (316.9 KiB/s) with 8 file(s) remaining\rCompleted 65.0 KiB/286.8 KiB (481.8 KiB/s) with 8 file(s) remaining\rupload: contents/Cappuccio2006 v9.0.sedml to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/Cappuccio2006 v9.0.sedml\nCompleted 65.0 KiB/286.8 KiB (481.8 KiB/s) with 7 file(s) remaining\rCompleted 65.2 KiB/286.8 KiB (453.3 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/curation_notes.txt\nCompleted 65.2 KiB/286.8 KiB (453.3 KiB/s) with 6 file(s) remaining\rCompleted 66.7 KiB/286.8 KiB (413.4 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/manifest.xml\nCompleted 66.7 KiB/286.8 KiB (413.4 KiB/s) with 5 file(s) remaining\rCompleted 68.5 KiB/286.8 KiB (407.9 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/metadata.rdf\nCompleted 68.5 KiB/286.8 KiB (407.9 KiB/s) with 4 file(s) remaining\rCompleted 94.3 KiB/286.8 KiB (528.0 KiB/s) with 4 file(s) remaining\rupload: contents/Cappuccio2006 v2.0-biopax3.owl to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/Cappuccio2006 v2.0-biopax3.owl\nCompleted 94.3 KiB/286.8 KiB (528.0 KiB/s) with 3 file(s) remaining\rCompleted 118.9 KiB/286.8 KiB (658.6 KiB/s) with 3 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/curation_image.png\nCompleted 118.9 KiB/286.8 KiB (658.6 KiB/s) with 2 file(s) remaining\rCompleted 194.3 KiB/286.8 KiB (1.0 MiB/s) with 2 file(s) remaining  \rupload: contents/Cappuccio2006 v2.0.xml to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/Cappuccio2006 v2.0.xml\nCompleted 194.3 KiB/286.8 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 286.8 KiB/286.8 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: contents/Cappuccio2006 v9.0.cps to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/contents/Cappuccio2006 v9.0.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.6 KiB/7.6 KiB (102.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711d0b9a62a8be53f8e934/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Cappuccio2006 v9.0.sedml\ncreating dataset /Cappuccio2006 v9.0.sedml/autogen_report_for_task1, shape: (44, 101), type: float64\ndataset created, uuid: d-ded2f182-cf80a760-5d5c-7bb527-cc16ce, chunk_size: (44, 101)\ncreating dataset /Cappuccio2006 v9.0.sedml/plot_1_task1, shape: (2, 101), type: float64\ndataset created, uuid: d-ded2f182-cf80a760-12ad-2cca24-afd726, chunk_size: (2, 101)\ncreating attribute combineArchiveLocation in /Cappuccio2006 v9.0.sedml\ncreating attribute uri in /Cappuccio2006 v9.0.sedml\ncreating attribute _type in /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\ncreating attribute uri in /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\ncreating attribute _type in /Cappuccio2006 v9.0.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Cappuccio2006 v9.0.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Cappuccio2006 v9.0.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Cappuccio2006 v9.0.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Cappuccio2006 v9.0.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Cappuccio2006 v9.0.sedml/plot_1_task1\ncreating attribute sedmlId in /Cappuccio2006 v9.0.sedml/plot_1_task1\ncreating attribute sedmlName in /Cappuccio2006 v9.0.sedml/plot_1_task1\ncreating attribute uri in /Cappuccio2006 v9.0.sedml/plot_1_task1\ncreate_links: /\ngot link: Cappuccio2006 v9.0.sedml\ncreate_links: /Cappuccio2006 v9.0.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Cappuccio2006 v9.0.sedml/autogen_report_for_task1 to tgt: /Cappuccio2006 v9.0.sedml/autogen_report_for_task1, shape: (44, 101), type: float64\niterating over chunks for /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 44, 1), slice(0, 101, 1))\ndone with dataload for /Cappuccio2006 v9.0.sedml/autogen_report_for_task1\nwrite_dataset src: /Cappuccio2006 v9.0.sedml/plot_1_task1 to tgt: /Cappuccio2006 v9.0.sedml/plot_1_task1, shape: (2, 101), type: float64\niterating over chunks for /Cappuccio2006 v9.0.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 101, 1))\ndone with dataload for /Cappuccio2006 v9.0.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711d0b9a62a8be53f8e934\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.155711,"sedDocuments":[{"location":"Cappuccio2006 v9.0.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  Cappuccio2006 v9.0.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      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: Cappuccio2006 v9.0.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":0.716908,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.154424,"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":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.311498,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.083724,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Z","status":"SUCCEEDED"},{"id":"autogen_task1_U","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_mu1","status":"SUCCEEDED"},{"id":"autogen_task1_h","status":"SUCCEEDED"},{"id":"autogen_task1_r1","status":"SUCCEEDED"},{"id":"autogen_task1_p1","status":"SUCCEEDED"},{"id":"autogen_task1_p2","status":"SUCCEEDED"},{"id":"autogen_task1_q1","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_mu2","status":"SUCCEEDED"},{"id":"autogen_task1_r2","status":"SUCCEEDED"},{"id":"autogen_task1_sigma","status":"SUCCEEDED"},{"id":"autogen_task1_h2zero","status":"SUCCEEDED"},{"id":"autogen_task1_D","status":"SUCCEEDED"},{"id":"autogen_task1_b1","status":"SUCCEEDED"},{"id":"autogen_task1_b2","status":"SUCCEEDED"},{"id":"autogen_task1_mu3","status":"SUCCEEDED"},{"id":"autogen_task1_r3","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_z0","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_IL_21_Clearance_Rate","status":"SUCCEEDED"},{"id":"autogen_task1_IL_21_Production_by_Tumor","status":"SUCCEEDED"},{"id":"autogen_task1_NK_Cell_Population_Growth","status":"SUCCEEDED"},{"id":"autogen_task1_NK_Cell_Population_Growth_IL_21_Inhibition","status":"SUCCEEDED"},{"id":"autogen_task1_CD8_Population_Growth","status":"SUCCEEDED"},{"id":"autogen_task1_CD8_Population_Growth_Inhibition","status":"SUCCEEDED"},{"id":"autogen_task1_CD8_Memory_Formation","status":"SUCCEEDED"},{"id":"autogen_task1_CD8_Memory_Loss","status":"SUCCEEDED"},{"id":"autogen_task1_Cytotoxic_Protein_Secretion","status":"SUCCEEDED"},{"id":"autogen_task1_Cytotoxic_Protein_Degradation","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Killing_By_NK_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Killing_By_CD8_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Growth_Exponential","status":"SUCCEEDED"}]}]}]}