{"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    447      0 --:--:-- --:--:-- --:--:--   448\n\r100  167k  100  167k    0     0   395k      0 --:--:-- --:--:-- --:--:--  395k\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 (24.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/rawLog.txt\nCompleted 2.5 KiB/2.5 KiB (36.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/MODEL1708240000.sedml/ (stored 0%)\n  adding: outputs/MODEL1708240000.sedml/plot_1_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 47%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 50.9 KiB/50.9 KiB (659.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/outputs/reports.h5\nCompleted 9.3 KiB/64.3 KiB (86.1 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/outputs/plots.zip\nCompleted 9.3 KiB/64.3 KiB (86.1 KiB/s) with 3 file(s) remaining\rCompleted 22.9 KiB/64.3 KiB (187.9 KiB/s) with 3 file(s) remaining\rupload: outputs/MODEL1708240000.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/outputs/MODEL1708240000.sedml/plot_1_task1.pdf\nCompleted 22.9 KiB/64.3 KiB (187.9 KiB/s) with 2 file(s) remaining\rCompleted 61.7 KiB/64.3 KiB (497.8 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/output.zip\nCompleted 61.7 KiB/64.3 KiB (497.8 KiB/s) with 1 file(s) remaining\rCompleted 64.3 KiB/64.3 KiB (508.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000670-biopax2.owl  \n  inflating: contents/BIOMD0000000670-biopax3.owl  \n  inflating: contents/BIOMD0000000670-matlab.m  \n  inflating: contents/BIOMD0000000670-octave.m  \n  inflating: contents/BIOMD0000000670.m  \n  inflating: contents/BIOMD0000000670.ode  \n  inflating: contents/BIOMD0000000670.pdf  \n  inflating: contents/BIOMD0000000670.png  \n  inflating: contents/BIOMD0000000670.sci  \n  inflating: contents/BIOMD0000000670.svg  \n  inflating: contents/BIOMD0000000670_url.xml  \n  inflating: contents/MODEL1708240000.cps  \n  inflating: contents/MODEL1708240000.sedml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 4.6 KiB/252.4 KiB (61.5 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000670-biopax3.owl to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670-biopax3.owl\nCompleted 4.6 KiB/252.4 KiB (61.5 KiB/s) with 16 file(s) remaining\rCompleted 8.0 KiB/252.4 KiB (73.3 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000670-matlab.m to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670-matlab.m\nCompleted 8.0 KiB/252.4 KiB (73.3 KiB/s) with 15 file(s) remaining\rCompleted 12.2 KiB/252.4 KiB (105.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000670-biopax2.owl to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670-biopax2.owl\nCompleted 12.2 KiB/252.4 KiB (105.1 KiB/s) with 14 file(s) remaining\rCompleted 13.7 KiB/252.4 KiB (105.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000670.sci to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670.sci\nCompleted 13.7 KiB/252.4 KiB (105.1 KiB/s) with 13 file(s) remaining\rCompleted 42.3 KiB/252.4 KiB (306.6 KiB/s) with 13 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/curation_image.jpeg\nCompleted 42.3 KiB/252.4 KiB (306.6 KiB/s) with 12 file(s) remaining\rCompleted 45.7 KiB/252.4 KiB (289.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000670-octave.m to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670-octave.m\nCompleted 45.7 KiB/252.4 KiB (289.5 KiB/s) with 11 file(s) remaining\rCompleted 47.6 KiB/252.4 KiB (285.4 KiB/s) with 11 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/manifest.xml\nCompleted 47.6 KiB/252.4 KiB (285.4 KiB/s) with 10 file(s) remaining\rCompleted 48.5 KiB/252.4 KiB (286.3 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000670.svg to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670.svg\nCompleted 48.5 KiB/252.4 KiB (286.3 KiB/s) with 9 file(s) remaining\rCompleted 67.6 KiB/252.4 KiB (393.9 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000670_url.xml to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670_url.xml\nCompleted 67.6 KiB/252.4 KiB (393.9 KiB/s) with 8 file(s) remaining\rCompleted 72.2 KiB/252.4 KiB (395.9 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/metadata.rdf\nCompleted 72.2 KiB/252.4 KiB (395.9 KiB/s) with 7 file(s) remaining\rCompleted 109.5 KiB/252.4 KiB (569.5 KiB/s) with 7 file(s) remaining\rupload: contents/MODEL1708240000.cps to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/MODEL1708240000.cps\nCompleted 109.5 KiB/252.4 KiB (569.5 KiB/s) with 6 file(s) remaining\rCompleted 117.8 KiB/252.4 KiB (602.9 KiB/s) with 6 file(s) remaining\rupload: contents/MODEL1708240000.sedml to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/MODEL1708240000.sedml\nCompleted 117.8 KiB/252.4 KiB (602.9 KiB/s) with 5 file(s) remaining\rCompleted 118.1 KiB/252.4 KiB (601.9 KiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/curation_notes.txt\nCompleted 118.1 KiB/252.4 KiB (601.9 KiB/s) with 4 file(s) remaining\rCompleted 122.3 KiB/252.4 KiB (614.4 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000670.png to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670.png\nCompleted 122.3 KiB/252.4 KiB (614.4 KiB/s) with 3 file(s) remaining\rCompleted 247.5 KiB/252.4 KiB (1.2 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000670.pdf to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670.pdf\nCompleted 247.5 KiB/252.4 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 250.9 KiB/252.4 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000670.m to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670.m\nCompleted 250.9 KiB/252.4 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 252.4 KiB/252.4 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000670.ode to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/contents/BIOMD0000000670.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.0 KiB/9.0 KiB (132.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c019a62a8be53f8cbc0/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /MODEL1708240000.sedml\ncreating dataset /MODEL1708240000.sedml/autogen_report_for_task1, shape: (13, 501), type: float64\ndataset created, uuid: d-7af0dcdb-d029c415-71cd-d481ec-b050e4, chunk_size: (13, 501)\ncreating dataset /MODEL1708240000.sedml/plot_1_task1, shape: (4, 501), type: float64\ndataset created, uuid: d-7af0dcdb-d029c415-879d-239d5c-62473e, chunk_size: (4, 501)\ncreating attribute combineArchiveLocation in /MODEL1708240000.sedml\ncreating attribute uri in /MODEL1708240000.sedml\ncreating attribute _type in /MODEL1708240000.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1708240000.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /MODEL1708240000.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /MODEL1708240000.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /MODEL1708240000.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /MODEL1708240000.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /MODEL1708240000.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /MODEL1708240000.sedml/autogen_report_for_task1\ncreating attribute uri in /MODEL1708240000.sedml/autogen_report_for_task1\ncreating attribute _type in /MODEL1708240000.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1708240000.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /MODEL1708240000.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /MODEL1708240000.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /MODEL1708240000.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /MODEL1708240000.sedml/plot_1_task1\ncreating attribute sedmlId in /MODEL1708240000.sedml/plot_1_task1\ncreating attribute sedmlName in /MODEL1708240000.sedml/plot_1_task1\ncreating attribute uri in /MODEL1708240000.sedml/plot_1_task1\ncreate_links: /\ngot link: MODEL1708240000.sedml\ncreate_links: /MODEL1708240000.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /MODEL1708240000.sedml/autogen_report_for_task1 to tgt: /MODEL1708240000.sedml/autogen_report_for_task1, shape: (13, 501), type: float64\niterating over chunks for /MODEL1708240000.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 501, 1))\ndone with dataload for /MODEL1708240000.sedml/autogen_report_for_task1\nwrite_dataset src: /MODEL1708240000.sedml/plot_1_task1 to tgt: /MODEL1708240000.sedml/plot_1_task1, shape: (4, 501), type: float64\niterating over chunks for /MODEL1708240000.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 501, 1))\ndone with dataload for /MODEL1708240000.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c019a62a8be53f8cbc0\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 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 the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.14764,"sedDocuments":[{"location":"MODEL1708240000.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  MODEL1708240000.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 13 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: MODEL1708240000.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":0.740421,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.116611,"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":0.397771,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.121441,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_l","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_K_l","status":"SUCCEEDED"},{"id":"autogen_task1_delta_l","status":"SUCCEEDED"},{"id":"autogen_task1_K_m","status":"SUCCEEDED"},{"id":"autogen_task1_xi","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"}]}]}]}