{"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    425      0 --:--:-- --:--:-- --:--:--   426\n\r  0  148k    0   581    0     0   1357      0  0:01:52 --:--:--  0:01:52  1357\r100  148k  100  148k    0     0   339k      0 --:--:-- --:--:-- --:--:-- 14.4M\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 (23.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (41.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/BIOMD0000000150_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000150_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 23%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 101.1 KiB/101.1 KiB (901.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/outputs/reports.h5\nCompleted 89.4 KiB/114.1 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/output.zip\nCompleted 89.4 KiB/114.1 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 92.1 KiB/114.1 KiB (818.4 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/rawLog.txt\nCompleted 92.1 KiB/114.1 KiB (818.4 KiB/s) with 2 file(s) remaining\rCompleted 105.3 KiB/114.1 KiB (914.7 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000150_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/outputs/BIOMD0000000150_url.sedml/autogen_plot_for_task1.pdf\nCompleted 105.3 KiB/114.1 KiB (914.7 KiB/s) with 1 file(s) remaining\rCompleted 114.1 KiB/114.1 KiB (981.0 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000150-biopax2.owl  \n  inflating: contents/BIOMD0000000150-biopax3.owl  \n  inflating: contents/BIOMD0000000150-matlab.m  \n  inflating: contents/BIOMD0000000150-octave.m  \n  inflating: contents/BIOMD0000000150.m  \n  inflating: contents/BIOMD0000000150.ode  \n  inflating: contents/BIOMD0000000150.pdf  \n  inflating: contents/BIOMD0000000150.png  \n  inflating: contents/BIOMD0000000150.svg  \n  inflating: contents/BIOMD0000000150.vcml  \n  inflating: contents/BIOMD0000000150_url.sedml  \n  inflating: contents/BIOMD0000000150_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 10.9 KiB/247.2 KiB (172.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000150-biopax3.owl to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150-biopax3.owl\nCompleted 10.9 KiB/247.2 KiB (172.2 KiB/s) with 15 file(s) remaining\rCompleted 11.0 KiB/247.2 KiB (95.3 KiB/s) with 15 file(s) remaining \rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/curation_notes.txt\nCompleted 11.0 KiB/247.2 KiB (95.3 KiB/s) with 14 file(s) remaining\rCompleted 14.8 KiB/247.2 KiB (120.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000150-matlab.m to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150-matlab.m\nCompleted 14.8 KiB/247.2 KiB (120.6 KiB/s) with 13 file(s) remaining\rCompleted 18.5 KiB/247.2 KiB (138.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000150-octave.m to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150-octave.m\nCompleted 18.5 KiB/247.2 KiB (138.6 KiB/s) with 12 file(s) remaining\rCompleted 25.6 KiB/247.2 KiB (188.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000150.svg to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150.svg\nCompleted 25.6 KiB/247.2 KiB (188.7 KiB/s) with 11 file(s) remaining\rCompleted 43.7 KiB/247.2 KiB (315.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000150.vcml to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150.vcml\nCompleted 43.7 KiB/247.2 KiB (315.3 KiB/s) with 10 file(s) remaining\rCompleted 50.7 KiB/247.2 KiB (359.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000150_url.sedml to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150_url.sedml\nCompleted 50.7 KiB/247.2 KiB (359.6 KiB/s) with 9 file(s) remaining\rCompleted 59.0 KiB/247.2 KiB (413.3 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000150-biopax2.owl to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150-biopax2.owl\nCompleted 59.0 KiB/247.2 KiB (413.3 KiB/s) with 8 file(s) remaining\rCompleted 60.9 KiB/247.2 KiB (377.1 KiB/s) with 8 file(s) remaining\rCompleted 74.9 KiB/247.2 KiB (460.3 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/curation_image.png\nCompleted 74.9 KiB/247.2 KiB (460.3 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/manifest.xml\nCompleted 74.9 KiB/247.2 KiB (460.3 KiB/s) with 6 file(s) remaining\rCompleted 77.2 KiB/247.2 KiB (432.2 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/metadata.rdf\nCompleted 77.2 KiB/247.2 KiB (432.2 KiB/s) with 5 file(s) remaining\rCompleted 79.4 KiB/247.2 KiB (393.0 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000150.ode to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150.ode\nCompleted 79.4 KiB/247.2 KiB (393.0 KiB/s) with 4 file(s) remaining\rCompleted 91.5 KiB/247.2 KiB (446.8 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000150.png to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150.png\nCompleted 91.5 KiB/247.2 KiB (446.8 KiB/s) with 3 file(s) remaining\rCompleted 95.2 KiB/247.2 KiB (458.5 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000150.m to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150.m\nCompleted 95.2 KiB/247.2 KiB (458.5 KiB/s) with 2 file(s) remaining\rCompleted 106.9 KiB/247.2 KiB (503.7 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000150_url.xml to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150_url.xml\nCompleted 106.9 KiB/247.2 KiB (503.7 KiB/s) with 1 file(s) remaining\rCompleted 247.2 KiB/247.2 KiB (1.1 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000150.pdf to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/contents/BIOMD0000000150.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (128.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108dc9a62a8be53f76dc5/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000150_url.sedml\ncreating dataset /BIOMD0000000150_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-07df1ecd-6b0a9579-e718-d111d3-7136a2, chunk_size: (5, 1001)\ncreating dataset /BIOMD0000000150_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-07df1ecd-6b0a9579-9c7e-97bea2-bce85e, chunk_size: (10, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000150_url.sedml\ncreating attribute uri in /BIOMD0000000150_url.sedml\ncreating attribute _type in /BIOMD0000000150_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000150_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000150_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000150_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000150_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000150_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000150_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000150_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000150_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000150_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000150_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000150_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000150_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000150_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000150_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000150_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000150_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000150_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000150_url.sedml\ncreate_links: /BIOMD0000000150_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000150_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000150_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\niterating over chunks for /BIOMD0000000150_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000150_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000150_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000150_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000150_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000150_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647108dc9a62a8be53f76dc5\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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.270954,"sedDocuments":[{"location":"BIOMD0000000150_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  BIOMD0000000150_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 10 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000150_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":0.850097,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.185389,"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":0.13547,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_CDK2cycA","status":"SUCCEEDED"},{"id":"autogen_task1_CyclinA","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk2","status":"SUCCEEDED"},{"id":"autogen_task1_CDK2cycA_star_","status":"SUCCEEDED"},{"id":"autogen_task1_basal_fluorescence","status":"SUCCEEDED"},{"id":"autogen_task1_total_fluorescence","status":"SUCCEEDED"},{"id":"autogen_task1_geometry","status":"SUCCEEDED"},{"id":"autogen_task1_Binding","status":"SUCCEEDED"},{"id":"autogen_task1_Activation","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.402694,"curves":[{"id":"autogen_curve_task1_CDK2cycA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CyclinA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cdk2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CDK2cycA_star_","status":"SUCCEEDED"}]}]}]}