{"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    452      0 --:--:-- --:--:-- --:--:--   452\n\r  0  166k    0   581    0     0   1369      0  0:02:04 --:--:--  0:02:04  1369\r100  166k  100  166k    0     0   380k      0 --:--:-- --:--:-- --:--:-- 13.4M\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 (17.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/rawLog.txt\nCompleted 6.4 KiB/6.4 KiB (77.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 85%)\n  adding: outputs/BIOMD0000000400_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000400_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 41%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 87.9 KiB/87.9 KiB (728.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/outputs/reports.h5\nCompleted 62.5 KiB/84.6 KiB (598.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/output.zip\nCompleted 62.5 KiB/84.6 KiB (598.3 KiB/s) with 3 file(s) remaining\rCompleted 70.3 KiB/84.6 KiB (644.9 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/outputs/plots.zip\nCompleted 70.3 KiB/84.6 KiB (644.9 KiB/s) with 2 file(s) remaining\rCompleted 73.0 KiB/84.6 KiB (569.5 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/rawLog.txt\nCompleted 73.0 KiB/84.6 KiB (569.5 KiB/s) with 1 file(s) remaining\rCompleted 84.6 KiB/84.6 KiB (559.6 KiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000400_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/outputs/BIOMD0000000400_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000400-biopax2.owl  \n  inflating: contents/BIOMD0000000400-biopax3.owl  \n  inflating: contents/BIOMD0000000400-matlab.m  \n  inflating: contents/BIOMD0000000400-octave.m  \n  inflating: contents/BIOMD0000000400.m  \n  inflating: contents/BIOMD0000000400.pdf  \n  inflating: contents/BIOMD0000000400.png  \n  inflating: contents/BIOMD0000000400.svg  \n  inflating: contents/BIOMD0000000400_url.sedml  \n  inflating: contents/BIOMD0000000400_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 10.7 KiB/324.4 KiB (155.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000400-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/BIOMD0000000400-biopax3.owl\nCompleted 10.7 KiB/324.4 KiB (155.6 KiB/s) with 13 file(s) remaining\rCompleted 20.2 KiB/324.4 KiB (176.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000400-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/BIOMD0000000400-biopax2.owl\nCompleted 20.2 KiB/324.4 KiB (176.1 KiB/s) with 12 file(s) remaining\rCompleted 56.4 KiB/324.4 KiB (418.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000400_url.sedml to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/BIOMD0000000400_url.sedml\nCompleted 56.4 KiB/324.4 KiB (418.0 KiB/s) with 11 file(s) remaining\rCompleted 234.4 KiB/324.4 KiB (1.5 MiB/s) with 11 file(s) remaining \rupload: contents/BIOMD0000000400.pdf to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/BIOMD0000000400.pdf\nCompleted 234.4 KiB/324.4 KiB (1.5 MiB/s) with 10 file(s) remaining\rCompleted 244.3 KiB/324.4 KiB (1.5 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000400-octave.m to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/BIOMD0000000400-octave.m\nCompleted 244.3 KiB/324.4 KiB (1.5 MiB/s) with 9 file(s) remaining\rCompleted 254.1 KiB/324.4 KiB (1.5 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000400-matlab.m to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/BIOMD0000000400-matlab.m\nCompleted 254.1 KiB/324.4 KiB (1.5 MiB/s) with 8 file(s) remaining\rCompleted 255.0 KiB/324.4 KiB (1.5 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000400.svg to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/BIOMD0000000400.svg\nCompleted 255.0 KiB/324.4 KiB (1.5 MiB/s) with 7 file(s) remaining\rCompleted 289.2 KiB/324.4 KiB (1.5 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000400_url.xml to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/BIOMD0000000400_url.xml\nCompleted 289.2 KiB/324.4 KiB (1.5 MiB/s) with 6 file(s) remaining\rCompleted 289.3 KiB/324.4 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/curation_notes.txt\nCompleted 289.3 KiB/324.4 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 299.2 KiB/324.4 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000400.m to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/BIOMD0000000400.m\nCompleted 299.2 KiB/324.4 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 300.8 KiB/324.4 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/manifest.xml\nCompleted 300.8 KiB/324.4 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 305.1 KiB/324.4 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000400.png to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/BIOMD0000000400.png\nCompleted 305.1 KiB/324.4 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 319.6 KiB/324.4 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/curation_image.png\nCompleted 319.6 KiB/324.4 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 324.4 KiB/324.4 KiB (893.4 KiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.2 KiB/8.2 KiB (77.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2177b6669655060cf7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000400_url.sedml\ncreating dataset /BIOMD0000000400_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-42fe30ed-075c3f5e-a1f4-af5822-ec9542, chunk_size: (14, 1001)\ncreating dataset /BIOMD0000000400_url.sedml/autogen_report_for_task1, shape: (70, 1001), type: float64\ndataset created, uuid: d-42fe30ed-075c3f5e-4184-42452d-8070e4, chunk_size: (70, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000400_url.sedml\ncreating attribute uri in /BIOMD0000000400_url.sedml\ncreating attribute _type in /BIOMD0000000400_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000400_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000400_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000400_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000400_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000400_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000400_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000400_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000400_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000400_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000400_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000400_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000400_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000400_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000400_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000400_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000400_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000400_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000400_url.sedml\ncreate_links: /BIOMD0000000400_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000400_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000400_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000400_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000400_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000400_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000400_url.sedml/autogen_report_for_task1, shape: (70, 1001), type: float64\niterating over chunks for /BIOMD0000000400_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 70, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000400_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b2177b6669655060cf7\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.982212,"sedDocuments":[{"location":"BIOMD0000000400_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  BIOMD0000000400_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 70 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 13 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000400_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":1.519606,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.296312,"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":0.474273,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Gd","status":"SUCCEEDED"},{"id":"autogen_task1_Gt","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_Rl","status":"SUCCEEDED"},{"id":"autogen_task1_Rg","status":"SUCCEEDED"},{"id":"autogen_task1_Rlg","status":"SUCCEEDED"},{"id":"autogen_task1_Rlgp","status":"SUCCEEDED"},{"id":"autogen_task1_IP3","status":"SUCCEEDED"},{"id":"autogen_task1_Pc","status":"SUCCEEDED"},{"id":"autogen_task1_Pcg","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_Pg","status":"SUCCEEDED"},{"id":"autogen_task1_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_L","status":"SUCCEEDED"},{"id":"autogen_task1_Ls","status":"SUCCEEDED"},{"id":"autogen_task1_ts","status":"SUCCEEDED"},{"id":"autogen_task1_PIP2","status":"SUCCEEDED"},{"id":"autogen_task1_J1","status":"SUCCEEDED"},{"id":"autogen_task1_kf1","status":"SUCCEEDED"},{"id":"autogen_task1_kr1","status":"SUCCEEDED"},{"id":"autogen_task1_Kd1","status":"SUCCEEDED"},{"id":"autogen_task1_J2","status":"SUCCEEDED"},{"id":"autogen_task1_kf2","status":"SUCCEEDED"},{"id":"autogen_task1_kr2","status":"SUCCEEDED"},{"id":"autogen_task1_Kd2","status":"SUCCEEDED"},{"id":"autogen_task1_J3","status":"SUCCEEDED"},{"id":"autogen_task1_kf3","status":"SUCCEEDED"},{"id":"autogen_task1_kr3","status":"SUCCEEDED"},{"id":"autogen_task1_J4","status":"SUCCEEDED"},{"id":"autogen_task1_kf4","status":"SUCCEEDED"},{"id":"autogen_task1_kr4","status":"SUCCEEDED"},{"id":"autogen_task1_Kd4","status":"SUCCEEDED"},{"id":"autogen_task1_J5","status":"SUCCEEDED"},{"id":"autogen_task1_kf5","status":"SUCCEEDED"},{"id":"autogen_task1_J6","status":"SUCCEEDED"},{"id":"autogen_task1_kf6","status":"SUCCEEDED"},{"id":"autogen_task1_J7","status":"SUCCEEDED"},{"id":"autogen_task1_kf7","status":"SUCCEEDED"},{"id":"autogen_task1_J8","status":"SUCCEEDED"},{"id":"autogen_task1_kf8","status":"SUCCEEDED"},{"id":"autogen_task1_kr8","status":"SUCCEEDED"},{"id":"autogen_task1_J9","status":"SUCCEEDED"},{"id":"autogen_task1_kf9","status":"SUCCEEDED"},{"id":"autogen_task1_kr9","status":"SUCCEEDED"},{"id":"autogen_task1_J10","status":"SUCCEEDED"},{"id":"autogen_task1_kf10","status":"SUCCEEDED"},{"id":"autogen_task1_kr10","status":"SUCCEEDED"},{"id":"autogen_task1_J11","status":"SUCCEEDED"},{"id":"autogen_task1_kf11","status":"SUCCEEDED"},{"id":"autogen_task1_kr11","status":"SUCCEEDED"},{"id":"autogen_task1_Kd11","status":"SUCCEEDED"},{"id":"autogen_task1_J12","status":"SUCCEEDED"},{"id":"autogen_task1_kf12","status":"SUCCEEDED"},{"id":"autogen_task1_J13","status":"SUCCEEDED"},{"id":"autogen_task1_kf13","status":"SUCCEEDED"},{"id":"autogen_task1_J14","status":"SUCCEEDED"},{"id":"autogen_task1_kf14","status":"SUCCEEDED"},{"id":"autogen_task1_Km14","status":"SUCCEEDED"},{"id":"autogen_task1_J15","status":"SUCCEEDED"},{"id":"autogen_task1_kf15","status":"SUCCEEDED"},{"id":"autogen_task1_Km15","status":"SUCCEEDED"},{"id":"autogen_task1_J16","status":"SUCCEEDED"},{"id":"autogen_task1_kf16","status":"SUCCEEDED"},{"id":"autogen_task1_Cpc","status":"SUCCEEDED"},{"id":"autogen_task1_Cc","status":"SUCCEEDED"},{"id":"autogen_task1_Cp","status":"SUCCEEDED"},{"id":"autogen_task1_Vc","status":"SUCCEEDED"},{"id":"autogen_task1_Rpc","status":"SUCCEEDED"},{"id":"autogen_task1_Compartment","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.57008,"curves":[{"id":"autogen_curve_task1_Gd","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Gt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Rl","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Rg","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Rlg","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Rlgp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IP3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pcg","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pg","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca","status":"SUCCEEDED"}]}]}]}