{"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    456      0 --:--:-- --:--:-- --:--:--   455\r100   139  100   139    0     0    451      0 --:--:-- --:--:-- --:--:--   451\n\r100  215k  100  215k    0     0   501k      0 --:--:-- --:--:-- --:--:--  501k\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 (27.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/rawLog.txt\nCompleted 4.1 KiB/4.1 KiB (67.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/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/BIOMD0000000193_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000193_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 179.4 KiB/179.4 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/outputs/reports.h5\nCompleted 168.7 KiB/192.3 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/output.zip\nCompleted 168.7 KiB/192.3 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 181.2 KiB/192.3 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000193_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/outputs/BIOMD0000000193_url.sedml/autogen_plot_for_task1.pdf\nCompleted 181.2 KiB/192.3 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 183.8 KiB/192.3 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/rawLog.txt\nCompleted 183.8 KiB/192.3 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 192.3 KiB/192.3 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000193-biopax2.owl  \n  inflating: contents/BIOMD0000000193-biopax3.owl  \n  inflating: contents/BIOMD0000000193-matlab.m  \n  inflating: contents/BIOMD0000000193-octave.m  \n  inflating: contents/BIOMD0000000193.m  \n  inflating: contents/BIOMD0000000193.ode  \n  inflating: contents/BIOMD0000000193.pdf  \n  inflating: contents/BIOMD0000000193.png  \n  inflating: contents/BIOMD0000000193.svg  \n  inflating: contents/BIOMD0000000193.vcml  \n  inflating: contents/BIOMD0000000193_url.sedml  \n  inflating: contents/BIOMD0000000193_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 25.8 KiB/407.4 KiB (350.8 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000193-biopax3.owl to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193-biopax3.owl\nCompleted 25.8 KiB/407.4 KiB (350.8 KiB/s) with 15 file(s) remaining\rCompleted 30.7 KiB/407.4 KiB (251.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000193-matlab.m to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193-matlab.m\nCompleted 30.7 KiB/407.4 KiB (251.7 KiB/s) with 14 file(s) remaining\rCompleted 48.3 KiB/407.4 KiB (360.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000193-biopax2.owl to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193-biopax2.owl\nCompleted 48.3 KiB/407.4 KiB (360.0 KiB/s) with 13 file(s) remaining\rCompleted 97.1 KiB/407.4 KiB (710.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000193.png to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193.png\nCompleted 97.1 KiB/407.4 KiB (710.6 KiB/s) with 12 file(s) remaining\rCompleted 98.9 KiB/407.4 KiB (710.6 KiB/s) with 12 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/manifest.xml\nCompleted 98.9 KiB/407.4 KiB (710.6 KiB/s) with 11 file(s) remaining\rCompleted 117.0 KiB/407.4 KiB (824.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000193.svg to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193.svg\nCompleted 117.0 KiB/407.4 KiB (824.8 KiB/s) with 10 file(s) remaining\rCompleted 152.9 KiB/407.4 KiB (1.0 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000193.vcml to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193.vcml\nCompleted 152.9 KiB/407.4 KiB (1.0 MiB/s) with 9 file(s) remaining\rCompleted 169.1 KiB/407.4 KiB (1.1 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000193_url.sedml to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193_url.sedml\nCompleted 169.1 KiB/407.4 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 193.0 KiB/407.4 KiB (1.2 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000193_url.xml to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193_url.xml\nCompleted 193.0 KiB/407.4 KiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 204.4 KiB/407.4 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/curation_image.png\nCompleted 204.4 KiB/407.4 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 204.6 KiB/407.4 KiB (1.1 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/curation_notes.txt\nCompleted 204.6 KiB/407.4 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 207.5 KiB/407.4 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/metadata.rdf\nCompleted 207.5 KiB/407.4 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 212.5 KiB/407.4 KiB (1011.6 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000193-octave.m to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193-octave.m\nCompleted 212.5 KiB/407.4 KiB (1011.6 KiB/s) with 3 file(s) remaining\rCompleted 215.7 KiB/407.4 KiB (1012.8 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000193.ode to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193.ode\nCompleted 215.7 KiB/407.4 KiB (1012.8 KiB/s) with 2 file(s) remaining\rCompleted 220.7 KiB/407.4 KiB (1.0 MiB/s) with 2 file(s) remaining   \rupload: contents/BIOMD0000000193.m to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193.m\nCompleted 220.7 KiB/407.4 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 407.4 KiB/407.4 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000193.pdf to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/contents/BIOMD0000000193.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (129.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471096d9a62a8be53f77e28/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000193_url.sedml\ncreating dataset /BIOMD0000000193_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-0e70c591-75612853-4b7d-3a7cae-b7203c, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000193_url.sedml/autogen_report_for_task1, shape: (28, 1001), type: float64\ndataset created, uuid: d-0e70c591-75612853-e9e2-1d2c8e-11a703, chunk_size: (28, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000193_url.sedml\ncreating attribute uri in /BIOMD0000000193_url.sedml\ncreating attribute _type in /BIOMD0000000193_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000193_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000193_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000193_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000193_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000193_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000193_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000193_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000193_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000193_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000193_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000193_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000193_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000193_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000193_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000193_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000193_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000193_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000193_url.sedml\ncreate_links: /BIOMD0000000193_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000193_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000193_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000193_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000193_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000193_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000193_url.sedml/autogen_report_for_task1, shape: (28, 1001), type: float64\niterating over chunks for /BIOMD0000000193_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 28, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000193_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471096d9a62a8be53f77e28\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.\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 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":1.321605,"sedDocuments":[{"location":"BIOMD0000000193_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  BIOMD0000000193_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 28 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000193_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":0.919789,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.186692,"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":0.19361,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Mad1_CMad2","status":"SUCCEEDED"},{"id":"autogen_task1_OMad2","status":"SUCCEEDED"},{"id":"autogen_task1_Mad1_CMad2_OMad2","status":"SUCCEEDED"},{"id":"autogen_task1_Cdc20","status":"SUCCEEDED"},{"id":"autogen_task1_Cdc20_CMad2","status":"SUCCEEDED"},{"id":"autogen_task1_Bub3_BubR1","status":"SUCCEEDED"},{"id":"autogen_task1_MCC","status":"SUCCEEDED"},{"id":"autogen_task1_Bub3_BubR1_Cdc20","status":"SUCCEEDED"},{"id":"autogen_task1_k3f","status":"SUCCEEDED"},{"id":"autogen_task1_kf6","status":"SUCCEEDED"},{"id":"autogen_task1_k5f","status":"SUCCEEDED"},{"id":"autogen_task1_k5r","status":"SUCCEEDED"},{"id":"autogen_task1_k2f","status":"SUCCEEDED"},{"id":"autogen_task1_k1f","status":"SUCCEEDED"},{"id":"autogen_task1_k1r","status":"SUCCEEDED"},{"id":"autogen_task1_k4f","status":"SUCCEEDED"},{"id":"autogen_task1_k4r","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_const_val_0","status":"SUCCEEDED"},{"id":"autogen_task1_const_val_1","status":"SUCCEEDED"},{"id":"autogen_task1_Cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"},{"id":"autogen_task1_R5","status":"SUCCEEDED"},{"id":"autogen_task1_R6","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.418683,"curves":[{"id":"autogen_curve_task1_Mad1_CMad2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OMad2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mad1_CMad2_OMad2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cdc20","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cdc20_CMad2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Bub3_BubR1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MCC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Bub3_BubR1_Cdc20","status":"SUCCEEDED"}]}]}]}