{"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    417      0 --:--:-- --:--:-- --:--:--   418\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  166k  100  166k    0     0   367k      0 --:--:-- --:--:-- --:--:-- 1509k\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 (15.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/rawLog.txt\nCompleted 2.4 KiB/2.4 KiB (25.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 71%)\n  adding: outputs/reports.h5 (deflated 54%)\n  adding: outputs/model.sedml/ (stored 0%)\n  adding: outputs/model.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 39.6 KiB/39.6 KiB (485.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/outputs/reports.h5\nCompleted 26.6 KiB/44.8 KiB (369.4 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/output.zip\nCompleted 26.6 KiB/44.8 KiB (369.4 KiB/s) with 3 file(s) remaining\rCompleted 29.3 KiB/44.8 KiB (273.2 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/rawLog.txt\nCompleted 29.3 KiB/44.8 KiB (273.2 KiB/s) with 2 file(s) remaining\rCompleted 35.4 KiB/44.8 KiB (253.0 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/outputs/plots.zip\nCompleted 35.4 KiB/44.8 KiB (253.0 KiB/s) with 1 file(s) remaining\rCompleted 44.8 KiB/44.8 KiB (313.6 KiB/s) with 1 file(s) remaining\rupload: outputs/model.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/outputs/model.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000531-biopax2.owl  \n  inflating: contents/BIOMD0000000531-biopax3.owl  \n  inflating: contents/BIOMD0000000531-matlab.m  \n  inflating: contents/BIOMD0000000531-octave.m  \n  inflating: contents/BIOMD0000000531.m  \n  inflating: contents/BIOMD0000000531.ode  \n  inflating: contents/BIOMD0000000531.pdf  \n  inflating: contents/BIOMD0000000531.png  \n  inflating: contents/BIOMD0000000531.svg  \n  inflating: contents/BIOMD0000000531.vcml  \n  inflating: contents/BIOMD0000000531_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/model.cps      \n  inflating: contents/model.sedml    \n  inflating: contents/manifest.xml   \nCompleted 4.6 KiB/232.7 KiB (65.4 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000531-biopax2.owl to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531-biopax2.owl\nCompleted 4.6 KiB/232.7 KiB (65.4 KiB/s) with 16 file(s) remaining\rCompleted 7.2 KiB/232.7 KiB (57.9 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000531-octave.m to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531-octave.m\nCompleted 7.2 KiB/232.7 KiB (57.9 KiB/s) with 15 file(s) remaining\rCompleted 9.9 KiB/232.7 KiB (72.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000531-matlab.m to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531-matlab.m\nCompleted 9.9 KiB/232.7 KiB (72.4 KiB/s) with 14 file(s) remaining\rCompleted 14.9 KiB/232.7 KiB (96.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000531.png to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531.png\nCompleted 14.9 KiB/232.7 KiB (96.6 KiB/s) with 13 file(s) remaining\rCompleted 16.9 KiB/232.7 KiB (107.1 KiB/s) with 13 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/manifest.xml\nCompleted 16.9 KiB/232.7 KiB (107.1 KiB/s) with 12 file(s) remaining\rCompleted 17.7 KiB/232.7 KiB (110.3 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000531.svg to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531.svg\nCompleted 17.7 KiB/232.7 KiB (110.3 KiB/s) with 11 file(s) remaining\rCompleted 29.2 KiB/232.7 KiB (177.1 KiB/s) with 11 file(s) remaining\rCompleted 44.3 KiB/232.7 KiB (263.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000531.vcml to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531.vcml\nCompleted 44.3 KiB/232.7 KiB (263.5 KiB/s) with 10 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/curation_image.png\nCompleted 44.3 KiB/232.7 KiB (263.5 KiB/s) with 9 file(s) remaining\rCompleted 49.4 KiB/232.7 KiB (271.2 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/metadata.rdf\nCompleted 49.4 KiB/232.7 KiB (271.2 KiB/s) with 8 file(s) remaining\rCompleted 62.8 KiB/232.7 KiB (326.2 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000531_url.xml to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531_url.xml\nCompleted 62.8 KiB/232.7 KiB (326.2 KiB/s) with 7 file(s) remaining\rCompleted 67.9 KiB/232.7 KiB (348.6 KiB/s) with 7 file(s) remaining\rupload: contents/model.sedml to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/model.sedml\nCompleted 67.9 KiB/232.7 KiB (348.6 KiB/s) with 6 file(s) remaining\rCompleted 68.0 KiB/232.7 KiB (327.0 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/curation_notes.txt\nCompleted 68.0 KiB/232.7 KiB (327.0 KiB/s) with 5 file(s) remaining\rCompleted 93.0 KiB/232.7 KiB (419.2 KiB/s) with 5 file(s) remaining\rupload: contents/model.cps to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/model.cps\nCompleted 93.0 KiB/232.7 KiB (419.2 KiB/s) with 4 file(s) remaining\rCompleted 97.8 KiB/232.7 KiB (430.3 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000531-biopax3.owl to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531-biopax3.owl\nCompleted 97.8 KiB/232.7 KiB (430.3 KiB/s) with 3 file(s) remaining\rCompleted 99.0 KiB/232.7 KiB (418.7 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000531.ode to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531.ode\nCompleted 99.0 KiB/232.7 KiB (418.7 KiB/s) with 2 file(s) remaining\rCompleted 100.9 KiB/232.7 KiB (377.9 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000531.m to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531.m\nCompleted 100.9 KiB/232.7 KiB (377.9 KiB/s) with 1 file(s) remaining\rCompleted 232.7 KiB/232.7 KiB (853.2 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000531.pdf to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/contents/BIOMD0000000531.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.0 KiB/9.0 KiB (126.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f14dda4ff2037f59beab/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /model.sedml\ncreating dataset /model.sedml/autogen_report_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-9c8a44ed-09afd90d-a1f1-84f406-a88241, chunk_size: (7, 1001)\ncreating dataset /model.sedml/plot_1_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-9c8a44ed-09afd90d-5ca5-18b675-2481d0, chunk_size: (2, 1001)\ncreating attribute combineArchiveLocation in /model.sedml\ncreating attribute uri in /model.sedml\ncreating attribute _type in /model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /model.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /model.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /model.sedml/autogen_report_for_task1\ncreating attribute uri in /model.sedml/autogen_report_for_task1\ncreating attribute _type in /model.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /model.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /model.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /model.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /model.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /model.sedml/plot_1_task1\ncreating attribute sedmlId in /model.sedml/plot_1_task1\ncreating attribute sedmlName in /model.sedml/plot_1_task1\ncreating attribute uri in /model.sedml/plot_1_task1\ncreate_links: /\ngot link: model.sedml\ncreate_links: /model.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /model.sedml/autogen_report_for_task1 to tgt: /model.sedml/autogen_report_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /model.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /model.sedml/autogen_report_for_task1\nwrite_dataset src: /model.sedml/plot_1_task1 to tgt: /model.sedml/plot_1_task1, shape: (2, 1001), type: float64\niterating over chunks for /model.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /model.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f14dda4ff2037f59beab\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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.110274,"sedDocuments":[{"location":"model.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  model.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 7 data sets\r\n    Plots (1):\r\n      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: model.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":0.726316,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.167305,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.344794,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.104004,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_Ka","status":"SUCCEEDED"},{"id":"autogen_task1_kb","status":"SUCCEEDED"},{"id":"autogen_task1_kat50","status":"SUCCEEDED"},{"id":"autogen_task1_v50t50","status":"SUCCEEDED"},{"id":"autogen_task1_Cell","status":"SUCCEEDED"}]}]}]}