{"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    382      0 --:--:-- --:--:-- --:--:--   382\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  609k  100  609k    0     0  1199k      0 --:--:-- --:--:-- --:--:-- 4381k\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 (14.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/rawLog.txt\nCompleted 4.1 KiB/4.1 KiB (44.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/BIOMD0000000441_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000441_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 214.0 KiB/214.0 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/outputs/reports.h5\nCompleted 200.6 KiB/220.6 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/output.zip\nCompleted 200.6 KiB/220.6 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 203.3 KiB/220.6 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/rawLog.txt\nCompleted 203.3 KiB/220.6 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 213.6 KiB/220.6 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000441_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/outputs/BIOMD0000000441_url.sedml/autogen_plot_for_task1.pdf\nCompleted 213.6 KiB/220.6 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 220.6 KiB/220.6 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000441-biopax2.owl  \n  inflating: contents/BIOMD0000000441-biopax3.owl  \n  inflating: contents/BIOMD0000000441-matlab.m  \n  inflating: contents/BIOMD0000000441.m  \n  inflating: contents/BIOMD0000000441.ode  \n  inflating: contents/BIOMD0000000441.pdf  \n  inflating: contents/BIOMD0000000441.png  \n  inflating: contents/BIOMD0000000441.svg  \n  inflating: contents/BIOMD0000000441.vcml  \n  inflating: contents/BIOMD0000000441_url.sedml  \n  inflating: contents/BIOMD0000000441_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 34.3 KiB/979.6 KiB (384.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000441-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441-biopax3.owl\nCompleted 34.3 KiB/979.6 KiB (384.3 KiB/s) with 14 file(s) remaining\rCompleted 59.6 KiB/979.6 KiB (431.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000441-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441-biopax2.owl\nCompleted 59.6 KiB/979.6 KiB (431.3 KiB/s) with 13 file(s) remaining\rCompleted 74.5 KiB/979.6 KiB (513.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000441_url.sedml to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441_url.sedml\nCompleted 74.5 KiB/979.6 KiB (513.8 KiB/s) with 12 file(s) remaining\rCompleted 83.6 KiB/979.6 KiB (567.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000441-matlab.m to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441-matlab.m\nCompleted 83.6 KiB/979.6 KiB (567.7 KiB/s) with 11 file(s) remaining\rCompleted 139.8 KiB/979.6 KiB (935.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000441.vcml to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441.vcml\nCompleted 139.8 KiB/979.6 KiB (935.4 KiB/s) with 10 file(s) remaining\rCompleted 140.0 KiB/979.6 KiB (864.3 KiB/s) with 10 file(s) remaining\rCompleted 197.1 KiB/979.6 KiB (1.2 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000441_url.xml to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441_url.xml\nCompleted 197.1 KiB/979.6 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/curation_notes.txt\nCompleted 197.1 KiB/979.6 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 204.0 KiB/979.6 KiB (1.2 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/metadata.rdf\nCompleted 204.0 KiB/979.6 KiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 256.2 KiB/979.6 KiB (1.4 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/curation_image.png\nCompleted 256.2 KiB/979.6 KiB (1.4 MiB/s) with 6 file(s) remaining\rCompleted 512.2 KiB/979.6 KiB (2.8 MiB/s) with 6 file(s) remaining\rCompleted 514.0 KiB/979.6 KiB (2.6 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/manifest.xml\nCompleted 514.0 KiB/979.6 KiB (2.6 MiB/s) with 5 file(s) remaining\rCompleted 520.8 KiB/979.6 KiB (2.4 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000441.ode to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441.ode\nCompleted 520.8 KiB/979.6 KiB (2.4 MiB/s) with 4 file(s) remaining\rCompleted 572.9 KiB/979.6 KiB (2.6 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000441.svg to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441.svg\nCompleted 572.9 KiB/979.6 KiB (2.6 MiB/s) with 3 file(s) remaining\rCompleted 808.5 KiB/979.6 KiB (3.5 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000441.pdf to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441.pdf\nCompleted 808.5 KiB/979.6 KiB (3.5 MiB/s) with 2 file(s) remaining\rCompleted 970.4 KiB/979.6 KiB (3.9 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000441.png to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441.png\nCompleted 970.4 KiB/979.6 KiB (3.9 MiB/s) with 1 file(s) remaining\rCompleted 979.6 KiB/979.6 KiB (3.7 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000441.m to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/contents/BIOMD0000000441.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (106.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b3277b6669655060d9f/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000441_url.sedml\ncreating dataset /BIOMD0000000441_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-cdfa6c99-7f28b112-c1ae-cf3b02-fafdc0, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000441_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\ndataset created, uuid: d-cdfa6c99-7f28b112-9c8a-a258d9-b1b828, chunk_size: (23, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000441_url.sedml\ncreating attribute uri in /BIOMD0000000441_url.sedml\ncreating attribute _type in /BIOMD0000000441_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000441_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000441_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000441_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000441_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000441_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000441_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000441_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000441_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000441_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000441_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000441_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000441_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000441_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000441_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000441_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000441_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000441_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000441_url.sedml\ncreate_links: /BIOMD0000000441_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000441_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000441_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000441_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000441_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000441_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000441_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\niterating over chunks for /BIOMD0000000441_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 23, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000441_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b3277b6669655060d9f\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.572942,"sedDocuments":[{"location":"BIOMD0000000441_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  BIOMD0000000441_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: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000441_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":1.124702,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.234355,"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":0.199938,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_species_0","status":"SUCCEEDED"},{"id":"autogen_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_task1_species_2","status":"SUCCEEDED"},{"id":"autogen_task1_species_3","status":"SUCCEEDED"},{"id":"autogen_task1_species_4","status":"SUCCEEDED"},{"id":"autogen_task1_species_5","status":"SUCCEEDED"},{"id":"autogen_task1_species_6","status":"SUCCEEDED"},{"id":"autogen_task1_species_7","status":"SUCCEEDED"},{"id":"autogen_task1_species_8","status":"SUCCEEDED"},{"id":"autogen_task1_species_9","status":"SUCCEEDED"},{"id":"autogen_task1_species_10","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_0","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_7","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_8","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_9","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.558087,"curves":[{"id":"autogen_curve_task1_species_0","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_5","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_6","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_7","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_8","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_9","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_10","status":"SUCCEEDED"}]}]}]}