{"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    429      0 --:--:-- --:--:-- --:--:--   429\n\r100  217k  100  217k    0     0   496k      0 --:--:-- --:--:-- --:--:--  496k\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 (25.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/rawLog.txt\nCompleted 3.0 KiB/3.0 KiB (48.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/BIOMD0000000307_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000307_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 79%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 28.4 KiB/28.4 KiB (381.1 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/outputs/reports.h5\nCompleted 14.1 KiB/31.2 KiB (194.4 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/output.zip\nCompleted 14.1 KiB/31.2 KiB (194.4 KiB/s) with 3 file(s) remaining\rCompleted 19.8 KiB/31.2 KiB (180.5 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/outputs/plots.zip\nCompleted 19.8 KiB/31.2 KiB (180.5 KiB/s) with 2 file(s) remaining\rCompleted 28.5 KiB/31.2 KiB (255.1 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000307_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/outputs/BIOMD0000000307_url.sedml/autogen_plot_for_task1.pdf\nCompleted 28.5 KiB/31.2 KiB (255.1 KiB/s) with 1 file(s) remaining\rCompleted 31.2 KiB/31.2 KiB (272.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000307-biopax2.owl  \n  inflating: contents/BIOMD0000000307-biopax3.owl  \n  inflating: contents/BIOMD0000000307-matlab.m  \n  inflating: contents/BIOMD0000000307-octave.m  \n  inflating: contents/BIOMD0000000307.m  \n  inflating: contents/BIOMD0000000307.ode  \n  inflating: contents/BIOMD0000000307.pdf  \n  inflating: contents/BIOMD0000000307.png  \n  inflating: contents/BIOMD0000000307.svg  \n  inflating: contents/BIOMD0000000307.vcml  \n  inflating: contents/BIOMD0000000307_url.sedml  \n  inflating: contents/BIOMD0000000307_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 13.2 KiB/355.2 KiB (176.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000307-biopax3.owl to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307-biopax3.owl\nCompleted 13.2 KiB/355.2 KiB (176.5 KiB/s) with 15 file(s) remaining\rCompleted 17.4 KiB/355.2 KiB (178.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000307-matlab.m to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307-matlab.m\nCompleted 17.4 KiB/355.2 KiB (178.3 KiB/s) with 14 file(s) remaining\rCompleted 19.3 KiB/355.2 KiB (142.0 KiB/s) with 14 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/manifest.xml\nCompleted 19.3 KiB/355.2 KiB (142.0 KiB/s) with 13 file(s) remaining\rCompleted 23.4 KiB/355.2 KiB (169.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000307-octave.m to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307-octave.m\nCompleted 23.4 KiB/355.2 KiB (169.8 KiB/s) with 12 file(s) remaining\rCompleted 34.1 KiB/355.2 KiB (231.2 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000307.svg to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307.svg\nCompleted 34.1 KiB/355.2 KiB (231.2 KiB/s) with 11 file(s) remaining\rCompleted 36.4 KiB/355.2 KiB (242.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000307.ode to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307.ode\nCompleted 36.4 KiB/355.2 KiB (242.5 KiB/s) with 10 file(s) remaining\rCompleted 40.0 KiB/355.2 KiB (263.7 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/metadata.rdf\nCompleted 40.0 KiB/355.2 KiB (263.7 KiB/s) with 9 file(s) remaining\rCompleted 49.9 KiB/355.2 KiB (315.7 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000307-biopax2.owl to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307-biopax2.owl\nCompleted 49.9 KiB/355.2 KiB (315.7 KiB/s) with 8 file(s) remaining\rCompleted 76.2 KiB/355.2 KiB (477.0 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000307.png to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307.png\nCompleted 76.2 KiB/355.2 KiB (477.0 KiB/s) with 7 file(s) remaining\rCompleted 80.3 KiB/355.2 KiB (494.2 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000307.m to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307.m\nCompleted 80.3 KiB/355.2 KiB (494.2 KiB/s) with 6 file(s) remaining\rCompleted 248.3 KiB/355.2 KiB (1.5 MiB/s) with 6 file(s) remaining \rupload: contents/BIOMD0000000307.pdf to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307.pdf\nCompleted 248.3 KiB/355.2 KiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 248.7 KiB/355.2 KiB (1.5 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/curation_notes.txt\nCompleted 248.7 KiB/355.2 KiB (1.5 MiB/s) with 4 file(s) remaining\rCompleted 268.1 KiB/355.2 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000307_url.xml to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307_url.xml\nCompleted 268.1 KiB/355.2 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 321.1 KiB/355.2 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 342.6 KiB/355.2 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000307.vcml to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307.vcml\nCompleted 342.6 KiB/355.2 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/curation_image.png\nCompleted 342.6 KiB/355.2 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 355.2 KiB/355.2 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000307_url.sedml to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/contents/BIOMD0000000307_url.sedml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (115.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a2794195afd5df1739253/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000307_url.sedml\ncreating dataset /BIOMD0000000307_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-acb3b0ea-bdb85e67-8537-b5e79f-d5f9c8, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000307_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\ndataset created, uuid: d-acb3b0ea-bdb85e67-069a-3ef8f5-1c8609, chunk_size: (23, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000307_url.sedml\ncreating attribute uri in /BIOMD0000000307_url.sedml\ncreating attribute _type in /BIOMD0000000307_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000307_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000307_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000307_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000307_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000307_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000307_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000307_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000307_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000307_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000307_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000307_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000307_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000307_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000307_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000307_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000307_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000307_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000307_url.sedml\ncreate_links: /BIOMD0000000307_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000307_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000307_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000307_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000307_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000307_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000307_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\niterating over chunks for /BIOMD0000000307_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 23, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000307_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a2794195afd5df1739253\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.242525,"sedDocuments":[{"location":"BIOMD0000000307_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  BIOMD0000000307_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 23 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000307_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":0.872412,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.142291,"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":0.209033,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_Ep","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_k0_prime","status":"SUCCEEDED"},{"id":"autogen_task1_k0","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_J3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_J4","status":"SUCCEEDED"},{"id":"autogen_task1_Et","status":"SUCCEEDED"},{"id":"autogen_task1_Km3","status":"SUCCEEDED"},{"id":"autogen_task1_Km4","status":"SUCCEEDED"},{"id":"autogen_task1_env","status":"SUCCEEDED"},{"id":"autogen_task1_r0","status":"SUCCEEDED"},{"id":"autogen_task1_r1","status":"SUCCEEDED"},{"id":"autogen_task1_r2","status":"SUCCEEDED"},{"id":"autogen_task1_r3","status":"SUCCEEDED"},{"id":"autogen_task1_r4","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.392436,"curves":[{"id":"autogen_curve_task1_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ep","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E","status":"SUCCEEDED"}]}]}]}