{"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    446      0 --:--:-- --:--:-- --:--:--   446\n\r100  195k  100  195k    0     0   462k      0 --:--:-- --:--:-- --:--:--  462k\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 (21.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/rawLog.txt\nCompleted 3.6 KiB/3.6 KiB (55.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000383_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000383_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/reports.h5 (deflated 29%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 74.5 KiB/74.5 KiB (851.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/outputs/reports.h5\nCompleted 62.8 KiB/83.2 KiB (720.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/output.zip\nCompleted 62.8 KiB/83.2 KiB (720.3 KiB/s) with 3 file(s) remaining\rCompleted 73.5 KiB/83.2 KiB (708.4 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000383_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/outputs/BIOMD0000000383_url.sedml/autogen_plot_for_task1.pdf\nCompleted 73.5 KiB/83.2 KiB (708.4 KiB/s) with 2 file(s) remaining\rCompleted 76.1 KiB/83.2 KiB (694.3 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/rawLog.txt\nCompleted 76.1 KiB/83.2 KiB (694.3 KiB/s) with 1 file(s) remaining\rCompleted 83.2 KiB/83.2 KiB (413.4 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000383-biopax2.owl  \n  inflating: contents/BIOMD0000000383-biopax3.owl  \n  inflating: contents/BIOMD0000000383-matlab.m  \n  inflating: contents/BIOMD0000000383-octave.m  \n  inflating: contents/BIOMD0000000383.m  \n  inflating: contents/BIOMD0000000383.ode  \n  inflating: contents/BIOMD0000000383.pdf  \n  inflating: contents/BIOMD0000000383.png  \n  inflating: contents/BIOMD0000000383.svg  \n  inflating: contents/BIOMD0000000383_url.sedml  \n  inflating: contents/BIOMD0000000383_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 16.1 KiB/321.3 KiB (232.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000383-biopax3.owl to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383-biopax3.owl\nCompleted 16.1 KiB/321.3 KiB (232.7 KiB/s) with 14 file(s) remaining\rCompleted 27.0 KiB/321.3 KiB (246.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000383-biopax2.owl to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383-biopax2.owl\nCompleted 27.0 KiB/321.3 KiB (246.9 KiB/s) with 13 file(s) remaining\rCompleted 32.0 KiB/321.3 KiB (275.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000383-matlab.m to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383-matlab.m\nCompleted 32.0 KiB/321.3 KiB (275.7 KiB/s) with 12 file(s) remaining\rCompleted 35.1 KiB/321.3 KiB (286.0 KiB/s) with 12 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/metadata.rdf\nCompleted 35.1 KiB/321.3 KiB (286.0 KiB/s) with 11 file(s) remaining\rCompleted 40.0 KiB/321.3 KiB (320.1 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000383-octave.m to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383-octave.m\nCompleted 40.0 KiB/321.3 KiB (320.1 KiB/s) with 10 file(s) remaining\rCompleted 53.2 KiB/321.3 KiB (395.4 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000383_url.sedml to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383_url.sedml\nCompleted 53.2 KiB/321.3 KiB (395.4 KiB/s) with 9 file(s) remaining\rCompleted 82.7 KiB/321.3 KiB (610.5 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000383_url.xml to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383_url.xml\nCompleted 82.7 KiB/321.3 KiB (610.5 KiB/s) with 8 file(s) remaining\rCompleted 105.3 KiB/321.3 KiB (675.5 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/curation_image.png\nCompleted 105.3 KiB/321.3 KiB (675.5 KiB/s) with 7 file(s) remaining\rCompleted 105.6 KiB/321.3 KiB (644.5 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/curation_notes.txt\nCompleted 105.6 KiB/321.3 KiB (644.5 KiB/s) with 6 file(s) remaining\rCompleted 107.3 KiB/321.3 KiB (572.8 KiB/s) with 6 file(s) remaining\rCompleted 112.3 KiB/321.3 KiB (592.0 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000383.m to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383.m\nCompleted 112.3 KiB/321.3 KiB (592.0 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/manifest.xml\nCompleted 112.3 KiB/321.3 KiB (592.0 KiB/s) with 4 file(s) remaining\rCompleted 115.4 KiB/321.3 KiB (588.0 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000383.ode to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383.ode\nCompleted 115.4 KiB/321.3 KiB (588.0 KiB/s) with 3 file(s) remaining\rCompleted 147.9 KiB/321.3 KiB (743.7 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000383.png to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383.png\nCompleted 147.9 KiB/321.3 KiB (743.7 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000383.svg to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383.svg\nCompleted 147.9 KiB/321.3 KiB (743.7 KiB/s) with 1 file(s) remaining\rCompleted 321.3 KiB/321.3 KiB (1.4 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000383.pdf to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/contents/BIOMD0000000383.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.4 KiB/8.4 KiB (136.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710bed49c0d898ffde20df/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000383_url.sedml\ncreating dataset /BIOMD0000000383_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-d7f3916e-90f688fe-da23-7a73f0-a093f6, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000383_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\ndataset created, uuid: d-d7f3916e-90f688fe-8016-97c6ec-f4a765, chunk_size: (23, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000383_url.sedml\ncreating attribute uri in /BIOMD0000000383_url.sedml\ncreating attribute _type in /BIOMD0000000383_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000383_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000383_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000383_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000383_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000383_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000383_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000383_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000383_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000383_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000383_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000383_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000383_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000383_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000383_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000383_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000383_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000383_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000383_url.sedml\ncreate_links: /BIOMD0000000383_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000383_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000383_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000383_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000383_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000383_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000383_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\niterating over chunks for /BIOMD0000000383_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 23, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000383_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710bed49c0d898ffde20df\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 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 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":1.287678,"sedDocuments":[{"location":"BIOMD0000000383_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  BIOMD0000000383_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 23 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000383_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 ... \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":0.873427,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.184993,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.177439,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_RuBP","status":"SUCCEEDED"},{"id":"autogen_task1_PGA","status":"SUCCEEDED"},{"id":"autogen_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_task1_CO2","status":"SUCCEEDED"},{"id":"autogen_task1_O2","status":"SUCCEEDED"},{"id":"autogen_task1_NADP","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_Rp","status":"SUCCEEDED"},{"id":"autogen_task1_Nt","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_jp","status":"SUCCEEDED"},{"id":"autogen_task1_j","status":"SUCCEEDED"},{"id":"autogen_task1_phi","status":"SUCCEEDED"},{"id":"autogen_task1_kc","status":"SUCCEEDED"},{"id":"autogen_task1_Kc","status":"SUCCEEDED"},{"id":"autogen_task1_Ko","status":"SUCCEEDED"},{"id":"autogen_task1_chloroplast","status":"SUCCEEDED"},{"id":"autogen_task1_PGA_prod_Vc","status":"SUCCEEDED"},{"id":"autogen_task1_PGA_prod_Vo","status":"SUCCEEDED"},{"id":"autogen_task1_PGA_cons","status":"SUCCEEDED"},{"id":"autogen_task1_NADPH_prod","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.359537,"curves":[{"id":"autogen_curve_task1_RuBP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PGA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CO2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADP","status":"SUCCEEDED"}]}]}]}