{"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    435      0 --:--:-- --:--:-- --:--:--   437\n\r100  266k  100  266k    0     0   581k      0 --:--:-- --:--:-- --:--:--  581k\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 (15.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (48.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000012_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000012_url.sedml/autogen_plot_for_task1.pdf (deflated 26%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/reports.h5 (deflated 13%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 212.7 KiB/212.7 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/outputs/reports.h5\nCompleted 194.7 KiB/215.7 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/output.zip\nCompleted 194.7 KiB/215.7 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 202.4 KiB/215.7 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/outputs/plots.zip\nCompleted 202.4 KiB/215.7 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 205.0 KiB/215.7 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/rawLog.txt\nCompleted 205.0 KiB/215.7 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 215.7 KiB/215.7 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000012_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/outputs/BIOMD0000000012_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/BIOMD0000000012-biopax2.owl  \n  inflating: contents/BIOMD0000000012-biopax3.owl  \n  inflating: contents/BIOMD0000000012-matlab.m  \n  inflating: contents/BIOMD0000000012-octave.m  \n  inflating: contents/BIOMD0000000012.m  \n  inflating: contents/BIOMD0000000012.ode  \n  inflating: contents/BIOMD0000000012.pdf  \n  inflating: contents/BIOMD0000000012.png  \n  inflating: contents/BIOMD0000000012.svg  \n  inflating: contents/BIOMD0000000012.vcml  \n  inflating: contents/BIOMD0000000012_manual.png  \n  inflating: contents/BIOMD0000000012_manual.svg  \n  inflating: contents/BIOMD0000000012_url.sedml  \n  inflating: contents/BIOMD0000000012_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 20.2 KiB/548.1 KiB (207.7 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000012-biopax3.owl to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012-biopax3.owl\nCompleted 20.2 KiB/548.1 KiB (207.7 KiB/s) with 17 file(s) remaining\rCompleted 25.8 KiB/548.1 KiB (230.1 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000012-matlab.m to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012-matlab.m\nCompleted 25.8 KiB/548.1 KiB (230.1 KiB/s) with 16 file(s) remaining\rCompleted 40.1 KiB/548.1 KiB (285.1 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000012-biopax2.owl to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012-biopax2.owl\nCompleted 40.1 KiB/548.1 KiB (285.1 KiB/s) with 15 file(s) remaining\rCompleted 45.7 KiB/548.1 KiB (294.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000012-octave.m to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012-octave.m\nCompleted 45.7 KiB/548.1 KiB (294.0 KiB/s) with 14 file(s) remaining\rCompleted 53.6 KiB/548.1 KiB (321.9 KiB/s) with 14 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/curation_image.png\nCompleted 53.6 KiB/548.1 KiB (321.9 KiB/s) with 13 file(s) remaining\rCompleted 111.4 KiB/548.1 KiB (658.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000012.vcml to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012.vcml\nCompleted 111.4 KiB/548.1 KiB (658.1 KiB/s) with 12 file(s) remaining\rCompleted 111.7 KiB/548.1 KiB (648.0 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/curation_notes.txt\nCompleted 111.7 KiB/548.1 KiB (648.0 KiB/s) with 11 file(s) remaining\rCompleted 146.6 KiB/548.1 KiB (830.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000012.svg to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012.svg\nCompleted 146.6 KiB/548.1 KiB (830.5 KiB/s) with 10 file(s) remaining\rCompleted 166.3 KiB/548.1 KiB (902.0 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000012_url.sedml to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012_url.sedml\nCompleted 166.3 KiB/548.1 KiB (902.0 KiB/s) with 9 file(s) remaining\rCompleted 201.2 KiB/548.1 KiB (1020.9 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000012_manual.svg to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012_manual.svg\nCompleted 201.2 KiB/548.1 KiB (1020.9 KiB/s) with 8 file(s) remaining\rCompleted 239.3 KiB/548.1 KiB (1.2 MiB/s) with 8 file(s) remaining   \rupload: contents/BIOMD0000000012_manual.png to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012_manual.png\nCompleted 239.3 KiB/548.1 KiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 284.4 KiB/548.1 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000012_url.xml to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012_url.xml\nCompleted 284.4 KiB/548.1 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 298.6 KiB/548.1 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/metadata.rdf\nCompleted 298.6 KiB/548.1 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 300.7 KiB/548.1 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/manifest.xml\nCompleted 300.7 KiB/548.1 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 304.7 KiB/548.1 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000012.ode to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012.ode\nCompleted 304.7 KiB/548.1 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 505.1 KiB/548.1 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000012.pdf to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012.pdf\nCompleted 505.1 KiB/548.1 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 510.0 KiB/548.1 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000012.m to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012.m\nCompleted 510.0 KiB/548.1 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 548.1 KiB/548.1 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000012.png to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/contents/BIOMD0000000012.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.5 KiB/9.5 KiB (104.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471071649c0d898ffdd8e1e/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000012_url.sedml\ncreating dataset /BIOMD0000000012_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-2b339897-702f97d9-dce6-10ed9d-e72a5e, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000012_url.sedml/autogen_report_for_task1, shape: (36, 1001), type: float64\ndataset created, uuid: d-2b339897-702f97d9-812f-72f03f-bfb540, chunk_size: (36, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000012_url.sedml\ncreating attribute uri in /BIOMD0000000012_url.sedml\ncreating attribute _type in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000012_url.sedml\ncreate_links: /BIOMD0000000012_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000012_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000012_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000012_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000012_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000012_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000012_url.sedml/autogen_report_for_task1, shape: (36, 1001), type: float64\niterating over chunks for /BIOMD0000000012_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 36, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000012_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471071649c0d898ffdd8e1e\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.530653,"sedDocuments":[{"location":"BIOMD0000000012_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  BIOMD0000000012_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 36 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000012_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":1.10439,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.184825,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.328476,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_PX","status":"SUCCEEDED"},{"id":"autogen_task1_PY","status":"SUCCEEDED"},{"id":"autogen_task1_PZ","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_Z","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_alpha0","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_eff","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_KM","status":"SUCCEEDED"},{"id":"autogen_task1_tau_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_tau_prot","status":"SUCCEEDED"},{"id":"autogen_task1_t_ave","status":"SUCCEEDED"},{"id":"autogen_task1_kd_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_kd_prot","status":"SUCCEEDED"},{"id":"autogen_task1_k_tl","status":"SUCCEEDED"},{"id":"autogen_task1_a_tr","status":"SUCCEEDED"},{"id":"autogen_task1_ps_a","status":"SUCCEEDED"},{"id":"autogen_task1_ps_0","status":"SUCCEEDED"},{"id":"autogen_task1_a0_tr","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction1","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction2","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction3","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction4","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction5","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction6","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction7","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction8","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction9","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction10","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction11","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction12","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.446108,"curves":[{"id":"autogen_curve_task1_PX","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PY","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PZ","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z","status":"SUCCEEDED"}]}]}]}