{"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    445      0 --:--:-- --:--:-- --:--:--   445\n\r100  173k  100  173k    0     0   395k      0 --:--:-- --:--:-- --:--:--  395k\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 (16.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/rawLog.txt\nCompleted 3.1 KiB/3.1 KiB (44.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/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/BIOMD0000000299_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000299_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 27%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 80.7 KiB/80.7 KiB (633.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/outputs/reports.h5\nCompleted 2.7 KiB/89.0 KiB (23.7 KiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/rawLog.txt\nCompleted 2.7 KiB/89.0 KiB (23.7 KiB/s) with 3 file(s) remaining\rCompleted 9.9 KiB/89.0 KiB (83.7 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/outputs/plots.zip\nCompleted 9.9 KiB/89.0 KiB (83.7 KiB/s) with 2 file(s) remaining\rCompleted 78.8 KiB/89.0 KiB (645.6 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/output.zip\nCompleted 78.8 KiB/89.0 KiB (645.6 KiB/s) with 1 file(s) remaining\rCompleted 89.0 KiB/89.0 KiB (738.3 KiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000299_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/outputs/BIOMD0000000299_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/BIOMD0000000299-biopax2.owl  \n  inflating: contents/BIOMD0000000299-biopax3.owl  \n  inflating: contents/BIOMD0000000299-matlab.m  \n  inflating: contents/BIOMD0000000299-octave.m  \n  inflating: contents/BIOMD0000000299.m  \n  inflating: contents/BIOMD0000000299.ode  \n  inflating: contents/BIOMD0000000299.pdf  \n  inflating: contents/BIOMD0000000299.png  \n  inflating: contents/BIOMD0000000299.sci  \n  inflating: contents/BIOMD0000000299.svg  \n  inflating: contents/BIOMD0000000299_url.sedml  \n  inflating: contents/BIOMD0000000299_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 5.3 KiB/247.3 KiB (57.8 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000299-biopax2.owl to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299-biopax2.owl\nCompleted 5.3 KiB/247.3 KiB (57.8 KiB/s) with 15 file(s) remaining\rCompleted 8.9 KiB/247.3 KiB (68.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000299-matlab.m to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299-matlab.m\nCompleted 8.9 KiB/247.3 KiB (68.3 KiB/s) with 14 file(s) remaining\rCompleted 12.5 KiB/247.3 KiB (81.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000299-octave.m to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299-octave.m\nCompleted 12.5 KiB/247.3 KiB (81.9 KiB/s) with 13 file(s) remaining\rCompleted 17.5 KiB/247.3 KiB (112.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000299.png to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299.png\nCompleted 17.5 KiB/247.3 KiB (112.8 KiB/s) with 12 file(s) remaining\rCompleted 18.9 KiB/247.3 KiB (115.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000299.sci to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299.sci\nCompleted 18.9 KiB/247.3 KiB (115.0 KiB/s) with 11 file(s) remaining\rCompleted 31.9 KiB/247.3 KiB (187.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000299_url.xml to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299_url.xml\nCompleted 31.9 KiB/247.3 KiB (187.7 KiB/s) with 10 file(s) remaining\rCompleted 41.5 KiB/247.3 KiB (230.4 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000299_url.sedml to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299_url.sedml\nCompleted 41.5 KiB/247.3 KiB (230.4 KiB/s) with 9 file(s) remaining\rCompleted 43.4 KiB/247.3 KiB (237.8 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/manifest.xml\nCompleted 43.4 KiB/247.3 KiB (237.8 KiB/s) with 8 file(s) remaining\rCompleted 44.2 KiB/247.3 KiB (238.5 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000299.svg to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299.svg\nCompleted 44.2 KiB/247.3 KiB (238.5 KiB/s) with 7 file(s) remaining\rCompleted 44.4 KiB/247.3 KiB (206.0 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/curation_notes.txt\nCompleted 44.4 KiB/247.3 KiB (206.0 KiB/s) with 6 file(s) remaining\rCompleted 49.8 KiB/247.3 KiB (225.3 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/metadata.rdf\nCompleted 49.8 KiB/247.3 KiB (225.3 KiB/s) with 5 file(s) remaining\rCompleted 90.8 KiB/247.3 KiB (406.0 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/curation_image.png\nCompleted 90.8 KiB/247.3 KiB (406.0 KiB/s) with 4 file(s) remaining\rCompleted 96.5 KiB/247.3 KiB (425.9 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000299-biopax3.owl to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299-biopax3.owl\nCompleted 96.5 KiB/247.3 KiB (425.9 KiB/s) with 3 file(s) remaining\rCompleted 98.2 KiB/247.3 KiB (374.9 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000299.ode to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299.ode\nCompleted 98.2 KiB/247.3 KiB (374.9 KiB/s) with 2 file(s) remaining\rCompleted 243.8 KiB/247.3 KiB (906.4 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000299.pdf to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299.pdf\nCompleted 243.8 KiB/247.3 KiB (906.4 KiB/s) with 1 file(s) remaining\rCompleted 247.3 KiB/247.3 KiB (663.1 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000299.m to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/contents/BIOMD0000000299.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (88.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f13a6262268786a35f1c/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000299_url.sedml\ncreating dataset /BIOMD0000000299_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-487d18a0-625e4e8a-e214-6eda07-fecc4f, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000299_url.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-487d18a0-625e4e8a-3c61-8f2b59-868e1a, chunk_size: (17, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000299_url.sedml\ncreating attribute uri in /BIOMD0000000299_url.sedml\ncreating attribute _type in /BIOMD0000000299_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000299_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000299_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000299_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000299_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000299_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000299_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000299_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000299_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000299_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000299_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000299_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000299_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000299_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000299_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000299_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000299_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000299_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000299_url.sedml\ncreate_links: /BIOMD0000000299_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000299_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000299_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000299_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000299_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000299_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000299_url.sedml/autogen_report_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /BIOMD0000000299_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000299_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f13a6262268786a35f1c\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 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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.363511,"sedDocuments":[{"location":"BIOMD0000000299_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  BIOMD0000000299_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: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000299_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":0.904707,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.198648,"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":0.162427,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_FC","status":"SUCCEEDED"},{"id":"autogen_task1_FN","status":"SUCCEEDED"},{"id":"autogen_task1_vs","status":"SUCCEEDED"},{"id":"autogen_task1_vm","status":"SUCCEEDED"},{"id":"autogen_task1_Km","status":"SUCCEEDED"},{"id":"autogen_task1_KI","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_Ft","status":"SUCCEEDED"},{"id":"autogen_task1_ks","status":"SUCCEEDED"},{"id":"autogen_task1_vd","status":"SUCCEEDED"},{"id":"autogen_task1_Kd","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_Cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_Nucleus","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.419702,"curves":[{"id":"autogen_curve_task1_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FN","status":"SUCCEEDED"}]}]}]}