{"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    439      0 --:--:-- --:--:-- --:--:--   439\n\r100  169k  100  169k    0     0   408k      0 --:--:-- --:--:-- --:--:--  408k\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 (22.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/rawLog.txt\nCompleted 3.5 KiB/3.5 KiB (34.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/BIOMD0000000077_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000077_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 172.8 KiB/172.8 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/outputs/reports.h5\nCompleted 162.5 KiB/184.8 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/output.zip\nCompleted 162.5 KiB/184.8 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 170.6 KiB/184.8 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/outputs/plots.zip\nCompleted 170.6 KiB/184.8 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 182.2 KiB/184.8 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000077_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/outputs/BIOMD0000000077_url.sedml/autogen_plot_for_task1.pdf\nCompleted 182.2 KiB/184.8 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 184.8 KiB/184.8 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000077-biopax2.owl  \n  inflating: contents/BIOMD0000000077-biopax3.owl  \n  inflating: contents/BIOMD0000000077-matlab.m  \n  inflating: contents/BIOMD0000000077-octave.m  \n  inflating: contents/BIOMD0000000077.m  \n  inflating: contents/BIOMD0000000077.ode  \n  inflating: contents/BIOMD0000000077.pdf  \n  inflating: contents/BIOMD0000000077.png  \n  inflating: contents/BIOMD0000000077.svg  \n  inflating: contents/BIOMD0000000077.vcml  \n  inflating: contents/BIOMD0000000077_url.sedml  \n  inflating: contents/BIOMD0000000077_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 14.8 KiB/322.1 KiB (181.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000077-biopax2.owl to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077-biopax2.owl\nCompleted 14.8 KiB/322.1 KiB (181.0 KiB/s) with 15 file(s) remaining\rCompleted 17.5 KiB/322.1 KiB (157.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000077.ode to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077.ode\nCompleted 17.5 KiB/322.1 KiB (157.0 KiB/s) with 14 file(s) remaining\rCompleted 22.3 KiB/322.1 KiB (163.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000077.m to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077.m\nCompleted 22.3 KiB/322.1 KiB (163.8 KiB/s) with 13 file(s) remaining\rCompleted 27.2 KiB/322.1 KiB (191.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000077-matlab.m to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077-matlab.m\nCompleted 27.2 KiB/322.1 KiB (191.8 KiB/s) with 12 file(s) remaining\rCompleted 46.6 KiB/322.1 KiB (323.1 KiB/s) with 12 file(s) remaining\rCompleted 57.2 KiB/322.1 KiB (393.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000077-biopax3.owl to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077-biopax3.owl\nCompleted 57.2 KiB/322.1 KiB (393.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000077_url.sedml to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077_url.sedml\nCompleted 57.2 KiB/322.1 KiB (393.7 KiB/s) with 10 file(s) remaining\rCompleted 62.1 KiB/322.1 KiB (425.1 KiB/s) with 10 file(s) remaining\rCompleted 88.0 KiB/322.1 KiB (598.0 KiB/s) with 10 file(s) remaining\rCompleted 249.4 KiB/322.1 KiB (1.6 MiB/s) with 10 file(s) remaining \rupload: contents/BIOMD0000000077-octave.m to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077-octave.m\nCompleted 249.4 KiB/322.1 KiB (1.6 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000077.png to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077.png\nCompleted 249.4 KiB/322.1 KiB (1.6 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000077.pdf to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077.pdf\nCompleted 249.4 KiB/322.1 KiB (1.6 MiB/s) with 7 file(s) remaining\rCompleted 249.5 KiB/322.1 KiB (1.6 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/curation_notes.txt\nCompleted 249.5 KiB/322.1 KiB (1.6 MiB/s) with 6 file(s) remaining\rCompleted 252.5 KiB/322.1 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/metadata.rdf\nCompleted 252.5 KiB/322.1 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 257.0 KiB/322.1 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 277.9 KiB/322.1 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000077_url.xml to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077_url.xml\nCompleted 277.9 KiB/322.1 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/curation_image.png\nCompleted 277.9 KiB/322.1 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 306.3 KiB/322.1 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000077.vcml to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077.vcml\nCompleted 306.3 KiB/322.1 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 308.2 KiB/322.1 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 322.1 KiB/322.1 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/manifest.xml\nCompleted 322.1 KiB/322.1 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000077.svg to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/contents/BIOMD0000000077.svg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (111.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c40b77b666965506a4e5/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000077_url.sedml\ncreating dataset /BIOMD0000000077_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-85938395-55b5e259-260a-a86b2d-a392bb, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000077_url.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-85938395-55b5e259-51f1-973d0f-a3c1f8, chunk_size: (17, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000077_url.sedml\ncreating attribute uri in /BIOMD0000000077_url.sedml\ncreating attribute _type in /BIOMD0000000077_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000077_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000077_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000077_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000077_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000077_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000077_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000077_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000077_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000077_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000077_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000077_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000077_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000077_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000077_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000077_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000077_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000077_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000077_url.sedml\ncreate_links: /BIOMD0000000077_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000077_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000077_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000077_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000077_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000077_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000077_url.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /BIOMD0000000077_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000077_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c40b77b666965506a4e5\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 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.352187,"sedDocuments":[{"location":"BIOMD0000000077_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  BIOMD0000000077_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 17 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000077_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":0.970812,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.195215,"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":0.172663,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_H","status":"SUCCEEDED"},{"id":"autogen_task1_HR","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_HRRH","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_GQ","status":"SUCCEEDED"},{"id":"autogen_task1_IP3","status":"SUCCEEDED"},{"id":"autogen_task1_CHO","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.49332,"curves":[{"id":"autogen_curve_task1_H","status":"SUCCEEDED"},{"id":"autogen_curve_task1_HR","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_HRRH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GQ","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IP3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CHO","status":"SUCCEEDED"}]}]}]}