{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    400      0 --:--:-- --:--:-- --:--:--   400\n\r100  207k  100  207k    0     0   437k      0 --:--:-- --:--:-- --:--:--  437k\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 (25.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/rawLog.txt\nCompleted 4.1 KiB/4.1 KiB (57.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/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/reports.h5 (deflated 14%)\n  adding: outputs/BIOMD0000000101_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000101_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 202.4 KiB/202.4 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/outputs/reports.h5\nCompleted 184.7 KiB/205.2 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/output.zip\nCompleted 184.7 KiB/205.2 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 191.8 KiB/205.2 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/outputs/plots.zip\nCompleted 191.8 KiB/205.2 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 202.5 KiB/205.2 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000101_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/outputs/BIOMD0000000101_url.sedml/autogen_plot_for_task1.pdf\nCompleted 202.5 KiB/205.2 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 205.2 KiB/205.2 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000101-biopax2.owl  \n  inflating: contents/BIOMD0000000101-biopax3.owl  \n  inflating: contents/BIOMD0000000101-matlab.m  \n  inflating: contents/BIOMD0000000101-octave.m  \n  inflating: contents/BIOMD0000000101.m  \n  inflating: contents/BIOMD0000000101.ode  \n  inflating: contents/BIOMD0000000101.pdf  \n  inflating: contents/BIOMD0000000101.png  \n  inflating: contents/BIOMD0000000101.svg  \n  inflating: contents/BIOMD0000000101.vcml  \n  inflating: contents/BIOMD0000000101_url.sedml  \n  inflating: contents/BIOMD0000000101_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 19.3 KiB/422.9 KiB (253.6 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000101-biopax2.owl to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101-biopax2.owl\nCompleted 19.3 KiB/422.9 KiB (253.6 KiB/s) with 15 file(s) remaining\rCompleted 24.4 KiB/422.9 KiB (219.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000101-octave.m to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101-octave.m\nCompleted 24.4 KiB/422.9 KiB (219.4 KiB/s) with 14 file(s) remaining\rCompleted 29.5 KiB/422.9 KiB (237.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000101-matlab.m to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101-matlab.m\nCompleted 29.5 KiB/422.9 KiB (237.7 KiB/s) with 13 file(s) remaining\rCompleted 88.4 KiB/422.9 KiB (656.4 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000101.png to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101.png\nCompleted 88.4 KiB/422.9 KiB (656.4 KiB/s) with 12 file(s) remaining\rCompleted 88.5 KiB/422.9 KiB (639.5 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/curation_notes.txt\nCompleted 88.5 KiB/422.9 KiB (639.5 KiB/s) with 11 file(s) remaining\rCompleted 112.1 KiB/422.9 KiB (769.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000101.svg to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101.svg\nCompleted 112.1 KiB/422.9 KiB (769.0 KiB/s) with 10 file(s) remaining\rCompleted 148.7 KiB/422.9 KiB (963.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000101.vcml to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101.vcml\nCompleted 148.7 KiB/422.9 KiB (963.7 KiB/s) with 9 file(s) remaining\rCompleted 151.7 KiB/422.9 KiB (921.3 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/metadata.rdf\nCompleted 151.7 KiB/422.9 KiB (921.3 KiB/s) with 8 file(s) remaining\rCompleted 168.5 KiB/422.9 KiB (1014.3 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000101_url.sedml to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101_url.sedml\nCompleted 168.5 KiB/422.9 KiB (1014.3 KiB/s) with 7 file(s) remaining\rCompleted 194.9 KiB/422.9 KiB (1.1 MiB/s) with 7 file(s) remaining   \rupload: contents/BIOMD0000000101_url.xml to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101_url.xml\nCompleted 194.9 KiB/422.9 KiB (1.1 MiB/s) with 6 file(s) remaining\rCompleted 208.3 KiB/422.9 KiB (1.1 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/curation_image.jpeg\nCompleted 208.3 KiB/422.9 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 210.2 KiB/422.9 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/manifest.xml\nCompleted 210.2 KiB/422.9 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 239.0 KiB/422.9 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000101-biopax3.owl to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101-biopax3.owl\nCompleted 239.0 KiB/422.9 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 244.1 KiB/422.9 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000101.m to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101.m\nCompleted 244.1 KiB/422.9 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 247.3 KiB/422.9 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000101.ode to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101.ode\nCompleted 247.3 KiB/422.9 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 422.9 KiB/422.9 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000101.pdf to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/contents/BIOMD0000000101.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (131.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471084449c0d898ffddb28d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000101_url.sedml\ncreating dataset /BIOMD0000000101_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-16c6de5a-a399b4b7-f022-852ea5-83606d, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000101_url.sedml/autogen_report_for_task1, shape: (31, 1001), type: float64\ndataset created, uuid: d-16c6de5a-a399b4b7-3a04-5423e2-6fbed7, chunk_size: (31, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000101_url.sedml\ncreating attribute uri in /BIOMD0000000101_url.sedml\ncreating attribute _type in /BIOMD0000000101_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000101_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000101_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000101_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000101_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000101_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000101_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000101_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000101_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000101_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000101_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000101_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000101_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000101_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000101_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000101_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000101_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000101_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000101_url.sedml\ncreate_links: /BIOMD0000000101_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000101_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000101_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000101_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000101_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000101_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000101_url.sedml/autogen_report_for_task1, shape: (31, 1001), type: float64\niterating over chunks for /BIOMD0000000101_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 31, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000101_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471084449c0d898ffddb28d\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.576777,"sedDocuments":[{"location":"BIOMD0000000101_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  BIOMD0000000101_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 31 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000101_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":1.09684,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.223617,"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":0.263868,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_RI","status":"SUCCEEDED"},{"id":"autogen_task1_RII","status":"SUCCEEDED"},{"id":"autogen_task1_lRIRII","status":"SUCCEEDED"},{"id":"autogen_task1_lRIRII_endo","status":"SUCCEEDED"},{"id":"autogen_task1_RI_endo","status":"SUCCEEDED"},{"id":"autogen_task1_RII_endo","status":"SUCCEEDED"},{"id":"autogen_task1_ka","status":"SUCCEEDED"},{"id":"autogen_task1_ligand","status":"SUCCEEDED"},{"id":"autogen_task1_kcd","status":"SUCCEEDED"},{"id":"autogen_task1_klid","status":"SUCCEEDED"},{"id":"autogen_task1_ki","status":"SUCCEEDED"},{"id":"autogen_task1_pRI","status":"SUCCEEDED"},{"id":"autogen_task1_kr","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_pRII","status":"SUCCEEDED"},{"id":"autogen_task1_PM","status":"SUCCEEDED"},{"id":"autogen_task1_Endosome","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"},{"id":"autogen_task1_v5","status":"SUCCEEDED"},{"id":"autogen_task1_v6","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"},{"id":"autogen_task1_v8","status":"SUCCEEDED"},{"id":"autogen_task1_v9","status":"SUCCEEDED"},{"id":"autogen_task1_v10","status":"SUCCEEDED"},{"id":"autogen_task1_v11","status":"SUCCEEDED"},{"id":"autogen_task1_v12","status":"SUCCEEDED"},{"id":"autogen_task1_v13","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.481449,"curves":[{"id":"autogen_curve_task1_RI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RII","status":"SUCCEEDED"},{"id":"autogen_curve_task1_lRIRII","status":"SUCCEEDED"},{"id":"autogen_curve_task1_lRIRII_endo","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RI_endo","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RII_endo","status":"SUCCEEDED"}]}]}]}