{"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    436      0 --:--:-- --:--:-- --:--:--   437\n\r100  205k  100  205k    0     0   467k      0 --:--:-- --:--:-- --:--:--  467k\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 (14.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/rawLog.txt\nCompleted 4.1 KiB/4.1 KiB (42.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/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/BIOMD0000000387_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000387_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 33%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 84.5 KiB/84.5 KiB (820.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/outputs/reports.h5\nCompleted 12.6 KiB/91.4 KiB (98.7 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000387_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/outputs/BIOMD0000000387_url.sedml/autogen_plot_for_task1.pdf\nCompleted 12.6 KiB/91.4 KiB (98.7 KiB/s) with 3 file(s) remaining\rCompleted 80.3 KiB/91.4 KiB (609.2 KiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/output.zip\nCompleted 80.3 KiB/91.4 KiB (609.2 KiB/s) with 2 file(s) remaining\rCompleted 88.8 KiB/91.4 KiB (631.2 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/outputs/plots.zip\nCompleted 88.8 KiB/91.4 KiB (631.2 KiB/s) with 1 file(s) remaining\rCompleted 91.4 KiB/91.4 KiB (597.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000387-biopax2.owl  \n  inflating: contents/BIOMD0000000387-biopax3.owl  \n  inflating: contents/BIOMD0000000387-matlab.m  \n  inflating: contents/BIOMD0000000387-octave.m  \n  inflating: contents/BIOMD0000000387.m  \n  inflating: contents/BIOMD0000000387.ode  \n  inflating: contents/BIOMD0000000387.pdf  \n  inflating: contents/BIOMD0000000387.png  \n  inflating: contents/BIOMD0000000387.svg  \n  inflating: contents/BIOMD0000000387_url.sedml  \n  inflating: contents/BIOMD0000000387_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 5.7 KiB/348.8 KiB (51.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000387-octave.m to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387-octave.m\nCompleted 5.7 KiB/348.8 KiB (51.6 KiB/s) with 14 file(s) remaining\rCompleted 17.0 KiB/348.8 KiB (153.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000387-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387-biopax2.owl\nCompleted 17.0 KiB/348.8 KiB (153.1 KiB/s) with 13 file(s) remaining\rCompleted 22.7 KiB/348.8 KiB (155.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000387-matlab.m to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387-matlab.m\nCompleted 22.7 KiB/348.8 KiB (155.6 KiB/s) with 12 file(s) remaining\rCompleted 34.7 KiB/348.8 KiB (210.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000387.svg to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387.svg\nCompleted 34.7 KiB/348.8 KiB (210.0 KiB/s) with 11 file(s) remaining\rCompleted 71.7 KiB/348.8 KiB (390.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000387.png to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387.png\nCompleted 71.7 KiB/348.8 KiB (390.5 KiB/s) with 10 file(s) remaining\rCompleted 88.4 KiB/348.8 KiB (471.0 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000387_url.sedml to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387_url.sedml\nCompleted 88.4 KiB/348.8 KiB (471.0 KiB/s) with 9 file(s) remaining\rCompleted 118.1 KiB/348.8 KiB (574.9 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000387_url.xml to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387_url.xml\nCompleted 118.1 KiB/348.8 KiB (574.9 KiB/s) with 8 file(s) remaining\rCompleted 294.8 KiB/348.8 KiB (1.3 MiB/s) with 8 file(s) remaining  \rupload: contents/BIOMD0000000387.pdf to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387.pdf\nCompleted 294.8 KiB/348.8 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 298.5 KiB/348.8 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/metadata.rdf\nCompleted 298.5 KiB/348.8 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 315.0 KiB/348.8 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000387-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387-biopax3.owl\nCompleted 315.0 KiB/348.8 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 337.5 KiB/348.8 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/curation_image.png\nCompleted 337.5 KiB/348.8 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 337.7 KiB/348.8 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/curation_notes.txt\nCompleted 337.7 KiB/348.8 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 339.4 KiB/348.8 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/manifest.xml\nCompleted 339.4 KiB/348.8 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 345.1 KiB/348.8 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000387.m to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387.m\nCompleted 345.1 KiB/348.8 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 348.8 KiB/348.8 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000387.ode to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/contents/BIOMD0000000387.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (81.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1c77b6669655060cde/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000387_url.sedml\ncreating dataset /BIOMD0000000387_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-8cdafb57-74bab41d-ddea-d846dd-8186ab, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000387_url.sedml/autogen_report_for_task1, shape: (30, 1001), type: float64\ndataset created, uuid: d-8cdafb57-74bab41d-10c9-3d86c6-cd4ae3, chunk_size: (30, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000387_url.sedml\ncreating attribute uri in /BIOMD0000000387_url.sedml\ncreating attribute _type in /BIOMD0000000387_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000387_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000387_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000387_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000387_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000387_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000387_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000387_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000387_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000387_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000387_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000387_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000387_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000387_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000387_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000387_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000387_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000387_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000387_url.sedml\ncreate_links: /BIOMD0000000387_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000387_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000387_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000387_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000387_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000387_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000387_url.sedml/autogen_report_for_task1, shape: (30, 1001), type: float64\niterating over chunks for /BIOMD0000000387_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 30, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000387_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b1c77b6669655060cde\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.\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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.72514,"sedDocuments":[{"location":"BIOMD0000000387_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  BIOMD0000000387_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 30 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000387_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":1.24525,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.262757,"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":0.257318,"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_starch","status":"SUCCEEDED"},{"id":"autogen_task1_Rp","status":"SUCCEEDED"},{"id":"autogen_task1_Nt","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_J","status":"SUCCEEDED"},{"id":"autogen_task1_Jmax","status":"SUCCEEDED"},{"id":"autogen_task1_Gamma","status":"SUCCEEDED"},{"id":"autogen_task1_Q","status":"SUCCEEDED"},{"id":"autogen_task1_Vcmax","status":"SUCCEEDED"},{"id":"autogen_task1_Kc","status":"SUCCEEDED"},{"id":"autogen_task1_Ko","status":"SUCCEEDED"},{"id":"autogen_task1_Vj","status":"SUCCEEDED"},{"id":"autogen_task1_phi","status":"SUCCEEDED"},{"id":"autogen_task1_Vc","status":"SUCCEEDED"},{"id":"autogen_task1_Vp","status":"SUCCEEDED"},{"id":"autogen_task1_TPU","status":"SUCCEEDED"},{"id":"autogen_task1_Cst","status":"SUCCEEDED"},{"id":"autogen_task1_a","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":0.563409,"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"},{"id":"autogen_curve_task1_starch","status":"SUCCEEDED"}]}]}]}