{"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    382      0 --:--:-- --:--:-- --:--:--   381\n\r100  136k  100  136k    0     0   293k      0 --:--:-- --:--:-- --:--:--  293k\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 (27.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/rawLog.txt\nCompleted 3.1 KiB/3.1 KiB (43.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/BIOMD0000000136_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000136_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 45%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 52.8 KiB/52.8 KiB (627.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/outputs/reports.h5\nCompleted 38.8 KiB/59.5 KiB (509.8 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/output.zip\nCompleted 38.8 KiB/59.5 KiB (509.8 KiB/s) with 3 file(s) remaining\rCompleted 41.5 KiB/59.5 KiB (393.7 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/rawLog.txt\nCompleted 41.5 KiB/59.5 KiB (393.7 KiB/s) with 2 file(s) remaining\rCompleted 48.7 KiB/59.5 KiB (456.9 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/outputs/plots.zip\nCompleted 48.7 KiB/59.5 KiB (456.9 KiB/s) with 1 file(s) remaining\rCompleted 59.5 KiB/59.5 KiB (544.1 KiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000136_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/outputs/BIOMD0000000136_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/BIOMD0000000136-biopax2.owl  \n  inflating: contents/BIOMD0000000136-biopax3.owl  \n  inflating: contents/BIOMD0000000136-matlab.m  \n  inflating: contents/BIOMD0000000136-octave.m  \n  inflating: contents/BIOMD0000000136.m  \n  inflating: contents/BIOMD0000000136.pdf  \n  inflating: contents/BIOMD0000000136.png  \n  inflating: contents/BIOMD0000000136.svg  \n  inflating: contents/BIOMD0000000136_url.sedml  \n  inflating: contents/BIOMD0000000136_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 3.7 KiB/197.1 KiB (52.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000136-biopax3.owl to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/BIOMD0000000136-biopax3.owl\nCompleted 3.7 KiB/197.1 KiB (52.6 KiB/s) with 13 file(s) remaining\rCompleted 7.1 KiB/197.1 KiB (72.0 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000136-matlab.m to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/BIOMD0000000136-matlab.m\nCompleted 7.1 KiB/197.1 KiB (72.0 KiB/s) with 12 file(s) remaining\rCompleted 10.6 KiB/197.1 KiB (91.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000136-biopax2.owl to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/BIOMD0000000136-biopax2.owl\nCompleted 10.6 KiB/197.1 KiB (91.8 KiB/s) with 11 file(s) remaining\rCompleted 15.7 KiB/197.1 KiB (120.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000136.png to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/BIOMD0000000136.png\nCompleted 15.7 KiB/197.1 KiB (120.0 KiB/s) with 10 file(s) remaining\rCompleted 22.8 KiB/197.1 KiB (170.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000136_url.sedml to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/BIOMD0000000136_url.sedml\nCompleted 22.8 KiB/197.1 KiB (170.6 KiB/s) with 9 file(s) remaining\rCompleted 26.2 KiB/197.1 KiB (193.5 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000136-octave.m to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/BIOMD0000000136-octave.m\nCompleted 26.2 KiB/197.1 KiB (193.5 KiB/s) with 8 file(s) remaining\rCompleted 38.7 KiB/197.1 KiB (282.2 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000136_url.xml to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/BIOMD0000000136_url.xml\nCompleted 38.7 KiB/197.1 KiB (282.2 KiB/s) with 7 file(s) remaining\rCompleted 53.8 KiB/197.1 KiB (356.8 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/curation_image.png\nCompleted 53.8 KiB/197.1 KiB (356.8 KiB/s) with 6 file(s) remaining\rCompleted 53.8 KiB/197.1 KiB (351.4 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/curation_notes.txt\nCompleted 53.8 KiB/197.1 KiB (351.4 KiB/s) with 5 file(s) remaining\rCompleted 54.7 KiB/197.1 KiB (334.4 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000136.svg to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/BIOMD0000000136.svg\nCompleted 54.7 KiB/197.1 KiB (334.4 KiB/s) with 4 file(s) remaining\rCompleted 58.4 KiB/197.1 KiB (351.0 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/metadata.rdf\nCompleted 58.4 KiB/197.1 KiB (351.0 KiB/s) with 3 file(s) remaining\rCompleted 60.0 KiB/197.1 KiB (352.6 KiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/manifest.xml\nCompleted 60.0 KiB/197.1 KiB (352.6 KiB/s) with 2 file(s) remaining\rCompleted 63.4 KiB/197.1 KiB (354.9 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000136.m to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/BIOMD0000000136.m\nCompleted 63.4 KiB/197.1 KiB (354.9 KiB/s) with 1 file(s) remaining\rCompleted 197.1 KiB/197.1 KiB (898.9 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000136.pdf to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/contents/BIOMD0000000136.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.2 KiB/8.2 KiB (123.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c43377b666965506a7fa/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000136_url.sedml\ncreating dataset /BIOMD0000000136_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-73d03a83-e91e831b-d9b4-88134e-1d50da, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000136_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-73d03a83-e91e831b-57c8-41b0cf-346d11, chunk_size: (10, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000136_url.sedml\ncreating attribute uri in /BIOMD0000000136_url.sedml\ncreating attribute _type in /BIOMD0000000136_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000136_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000136_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000136_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000136_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000136_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000136_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000136_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000136_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000136_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000136_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000136_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000136_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000136_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000136_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000136_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000136_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000136_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000136_url.sedml\ncreate_links: /BIOMD0000000136_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000136_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000136_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000136_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000136_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000136_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000136_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000136_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000136_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c43377b666965506a7fa\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":1.157438,"sedDocuments":[{"location":"BIOMD0000000136_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  BIOMD0000000136_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: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000136_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":0.787672,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.151675,"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":0.111985,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_Vthresh","status":"SUCCEEDED"},{"id":"autogen_task1_i","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.408643,"curves":[{"id":"autogen_curve_task1_a","status":"SUCCEEDED"},{"id":"autogen_curve_task1_b","status":"SUCCEEDED"},{"id":"autogen_curve_task1_c","status":"SUCCEEDED"},{"id":"autogen_curve_task1_d","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Vthresh","status":"SUCCEEDED"},{"id":"autogen_curve_task1_i","status":"SUCCEEDED"},{"id":"autogen_curve_task1_v","status":"SUCCEEDED"},{"id":"autogen_curve_task1_u","status":"SUCCEEDED"}]}]}]}