{"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    440      0 --:--:-- --:--:-- --:--:--   441\n\r100  261k  100  261k    0     0   588k      0 --:--:-- --:--:-- --:--:--  588k\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/647a4b1877b6669655060cd2/rawLog.txt\nCompleted 6.4 KiB/6.4 KiB (64.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000379_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000379_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/log.yml (deflated 84%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/303.6 KiB (5.4 MiB/s) with 1 file(s) remaining\rCompleted 303.6 KiB/303.6 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/outputs/reports.h5\nCompleted 256.0 KiB/304.0 KiB (5.6 MiB/s) with 4 file(s) remaining\rCompleted 279.5 KiB/304.0 KiB (2.6 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/output.zip\nCompleted 279.5 KiB/304.0 KiB (2.6 MiB/s) with 3 file(s) remaining\rCompleted 292.4 KiB/304.0 KiB (2.4 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000379_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/outputs/BIOMD0000000379_url.sedml/autogen_plot_for_task1.pdf\nCompleted 292.4 KiB/304.0 KiB (2.4 MiB/s) with 2 file(s) remaining\rCompleted 301.3 KiB/304.0 KiB (2.4 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/outputs/plots.zip\nCompleted 301.3 KiB/304.0 KiB (2.4 MiB/s) with 1 file(s) remaining\rCompleted 304.0 KiB/304.0 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000379-biopax2.owl  \n  inflating: contents/BIOMD0000000379-biopax3.owl  \n  inflating: contents/BIOMD0000000379-matlab.m  \n  inflating: contents/BIOMD0000000379-octave.m  \n  inflating: contents/BIOMD0000000379.m  \n  inflating: contents/BIOMD0000000379.ode  \n  inflating: contents/BIOMD0000000379.pdf  \n  inflating: contents/BIOMD0000000379.png  \n  inflating: contents/BIOMD0000000379.svg  \n  inflating: contents/BIOMD0000000379_url.sedml  \n  inflating: contents/BIOMD0000000379_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 5.4 KiB/418.9 KiB (53.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000379-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379-biopax2.owl\nCompleted 5.4 KiB/418.9 KiB (53.5 KiB/s) with 14 file(s) remaining\rCompleted 12.1 KiB/418.9 KiB (95.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000379-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379-biopax3.owl\nCompleted 12.1 KiB/418.9 KiB (95.8 KiB/s) with 13 file(s) remaining\rCompleted 48.8 KiB/418.9 KiB (318.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000379_url.sedml to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379_url.sedml\nCompleted 48.8 KiB/418.9 KiB (318.8 KiB/s) with 12 file(s) remaining\rCompleted 53.9 KiB/418.9 KiB (343.6 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000379.png to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379.png\nCompleted 53.9 KiB/418.9 KiB (343.6 KiB/s) with 11 file(s) remaining\rCompleted 54.7 KiB/418.9 KiB (341.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000379.svg to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379.svg\nCompleted 54.7 KiB/418.9 KiB (341.7 KiB/s) with 10 file(s) remaining\rCompleted 86.4 KiB/418.9 KiB (462.2 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000379_url.xml to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379_url.xml\nCompleted 86.4 KiB/418.9 KiB (462.2 KiB/s) with 9 file(s) remaining\rCompleted 90.3 KiB/418.9 KiB (478.3 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/metadata.rdf\nCompleted 90.3 KiB/418.9 KiB (478.3 KiB/s) with 8 file(s) remaining\rCompleted 92.0 KiB/418.9 KiB (465.5 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/manifest.xml\nCompleted 92.0 KiB/418.9 KiB (465.5 KiB/s) with 7 file(s) remaining\rCompleted 213.2 KiB/418.9 KiB (1004.9 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/curation_image.png\nCompleted 213.2 KiB/418.9 KiB (1004.9 KiB/s) with 6 file(s) remaining\rCompleted 213.4 KiB/418.9 KiB (995.2 KiB/s) with 6 file(s) remaining \rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/curation_notes.txt\nCompleted 213.4 KiB/418.9 KiB (995.2 KiB/s) with 5 file(s) remaining\rCompleted 223.0 KiB/418.9 KiB (983.1 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000379-matlab.m to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379-matlab.m\nCompleted 223.0 KiB/418.9 KiB (983.1 KiB/s) with 4 file(s) remaining\rCompleted 393.0 KiB/418.9 KiB (1.6 MiB/s) with 4 file(s) remaining  \rupload: contents/BIOMD0000000379.pdf to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379.pdf\nCompleted 393.0 KiB/418.9 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 402.6 KiB/418.9 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000379-octave.m to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379-octave.m\nCompleted 402.6 KiB/418.9 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 409.3 KiB/418.9 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000379.ode to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379.ode\nCompleted 409.3 KiB/418.9 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 418.9 KiB/418.9 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000379.m to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/contents/BIOMD0000000379.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (81.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1877b6669655060cd2/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000379_url.sedml\ncreating dataset /BIOMD0000000379_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\ndataset created, uuid: d-55d5c617-8ea4d2c9-9358-216300-484760, chunk_size: (13, 1001)\ncreating dataset /BIOMD0000000379_url.sedml/autogen_report_for_task1, shape: (71, 1001), type: float64\ndataset created, uuid: d-55d5c617-8ea4d2c9-9145-3cb5db-3199e7, chunk_size: (71, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000379_url.sedml\ncreating attribute uri in /BIOMD0000000379_url.sedml\ncreating attribute _type in /BIOMD0000000379_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000379_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000379_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000379_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000379_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000379_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000379_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000379_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000379_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000379_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000379_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000379_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000379_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000379_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000379_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000379_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000379_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000379_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000379_url.sedml\ncreate_links: /BIOMD0000000379_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000379_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000379_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\niterating over chunks for /BIOMD0000000379_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000379_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000379_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000379_url.sedml/autogen_report_for_task1, shape: (71, 1001), type: float64\niterating over chunks for /BIOMD0000000379_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 71, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000379_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b1877b6669655060cd2\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 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 and upload the outputs of the simulation run ... 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":2.129556,"sedDocuments":[{"location":"BIOMD0000000379_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  BIOMD0000000379_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 71 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000379_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":1.594085,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.307829,"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":0.511898,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_G_p","status":"SUCCEEDED"},{"id":"autogen_task1_G_t","status":"SUCCEEDED"},{"id":"autogen_task1_I_l","status":"SUCCEEDED"},{"id":"autogen_task1_I_p","status":"SUCCEEDED"},{"id":"autogen_task1_Q_sto1","status":"SUCCEEDED"},{"id":"autogen_task1_Q_gut","status":"SUCCEEDED"},{"id":"autogen_task1_I_1","status":"SUCCEEDED"},{"id":"autogen_task1_I_d","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_I_po","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_Q_sto2","status":"SUCCEEDED"},{"id":"autogen_task1_V_G","status":"SUCCEEDED"},{"id":"autogen_task1_k_1","status":"SUCCEEDED"},{"id":"autogen_task1_k_2","status":"SUCCEEDED"},{"id":"autogen_task1_G_b","status":"SUCCEEDED"},{"id":"autogen_task1_V_I","status":"SUCCEEDED"},{"id":"autogen_task1_m_1","status":"SUCCEEDED"},{"id":"autogen_task1_m_2","status":"SUCCEEDED"},{"id":"autogen_task1_m_4","status":"SUCCEEDED"},{"id":"autogen_task1_m_5","status":"SUCCEEDED"},{"id":"autogen_task1_m_6","status":"SUCCEEDED"},{"id":"autogen_task1_HE_b","status":"SUCCEEDED"},{"id":"autogen_task1_I_b","status":"SUCCEEDED"},{"id":"autogen_task1_S_b","status":"SUCCEEDED"},{"id":"autogen_task1_S_b_minus","status":"SUCCEEDED"},{"id":"autogen_task1_k_max","status":"SUCCEEDED"},{"id":"autogen_task1_k_min","status":"SUCCEEDED"},{"id":"autogen_task1_k_abs","status":"SUCCEEDED"},{"id":"autogen_task1_k_gri","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_BW","status":"SUCCEEDED"},{"id":"autogen_task1_k_p1","status":"SUCCEEDED"},{"id":"autogen_task1_k_p2","status":"SUCCEEDED"},{"id":"autogen_task1_k_p3","status":"SUCCEEDED"},{"id":"autogen_task1_k_p4","status":"SUCCEEDED"},{"id":"autogen_task1_k_i","status":"SUCCEEDED"},{"id":"autogen_task1_U_ii","status":"SUCCEEDED"},{"id":"autogen_task1_V_m0","status":"SUCCEEDED"},{"id":"autogen_task1_V_mX","status":"SUCCEEDED"},{"id":"autogen_task1_K_m0","status":"SUCCEEDED"},{"id":"autogen_task1_p_2U","status":"SUCCEEDED"},{"id":"autogen_task1_part","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_k_e1","status":"SUCCEEDED"},{"id":"autogen_task1_k_e2","status":"SUCCEEDED"},{"id":"autogen_task1_D","status":"SUCCEEDED"},{"id":"autogen_task1_aa","status":"SUCCEEDED"},{"id":"autogen_task1_cc","status":"SUCCEEDED"},{"id":"autogen_task1_EGP","status":"SUCCEEDED"},{"id":"autogen_task1_V_mmax","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_G","status":"SUCCEEDED"},{"id":"autogen_task1_HE","status":"SUCCEEDED"},{"id":"autogen_task1_m_3","status":"SUCCEEDED"},{"id":"autogen_task1_Q_sto","status":"SUCCEEDED"},{"id":"autogen_task1_Ra","status":"SUCCEEDED"},{"id":"autogen_task1_k_empt","status":"SUCCEEDED"},{"id":"autogen_task1_U_idm","status":"SUCCEEDED"},{"id":"autogen_task1_U_id","status":"SUCCEEDED"},{"id":"autogen_task1_U","status":"SUCCEEDED"},{"id":"autogen_task1_S_po","status":"SUCCEEDED"},{"id":"autogen_task1_Compartment1","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.598374,"curves":[{"id":"autogen_curve_task1_G_p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G_t","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I_l","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I_p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Q_sto1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Q_gut","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I_d","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I_po","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Q_sto2","status":"SUCCEEDED"}]}]}]}