{"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    472      0 --:--:-- --:--:-- --:--:--   472\n\r100  159k  100  159k    0     0   382k      0 --:--:-- --:--:-- --:--:--  382k\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 (15.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/rawLog.txt\nCompleted 2.5 KiB/2.5 KiB (10.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/BIOMD0000000417_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000417_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 41%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 48.1 KiB/48.1 KiB (563.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/outputs/reports.h5\nCompleted 38.1 KiB/59.1 KiB (345.4 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/output.zip\nCompleted 38.1 KiB/59.1 KiB (345.4 KiB/s) with 3 file(s) remaining\rCompleted 40.7 KiB/59.1 KiB (282.3 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/rawLog.txt\nCompleted 40.7 KiB/59.1 KiB (282.3 KiB/s) with 2 file(s) remaining\rCompleted 48.2 KiB/59.1 KiB (321.2 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/outputs/plots.zip\nCompleted 48.2 KiB/59.1 KiB (321.2 KiB/s) with 1 file(s) remaining\rCompleted 59.1 KiB/59.1 KiB (365.7 KiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000417_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/outputs/BIOMD0000000417_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/BIOMD0000000417-biopax2.owl  \n  inflating: contents/BIOMD0000000417-biopax3.owl  \n  inflating: contents/BIOMD0000000417-matlab.m  \n  inflating: contents/BIOMD0000000417-octave.m  \n  inflating: contents/BIOMD0000000417.m  \n  inflating: contents/BIOMD0000000417.ode  \n  inflating: contents/BIOMD0000000417.pdf  \n  inflating: contents/BIOMD0000000417.png  \n  inflating: contents/BIOMD0000000417.sci  \n  inflating: contents/BIOMD0000000417.svg  \n  inflating: contents/BIOMD0000000417.vcml  \n  inflating: contents/BIOMD0000000417_url.sedml  \n  inflating: contents/BIOMD0000000417_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 5.7 KiB/244.3 KiB (57.9 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000417-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417-biopax3.owl\nCompleted 5.7 KiB/244.3 KiB (57.9 KiB/s) with 16 file(s) remaining\rCompleted 9.2 KiB/244.3 KiB (68.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000417-matlab.m to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417-matlab.m\nCompleted 9.2 KiB/244.3 KiB (68.5 KiB/s) with 15 file(s) remaining\rCompleted 11.4 KiB/244.3 KiB (77.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000417.sci to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417.sci\nCompleted 11.4 KiB/244.3 KiB (77.6 KiB/s) with 14 file(s) remaining\rCompleted 15.0 KiB/244.3 KiB (99.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000417-octave.m to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417-octave.m\nCompleted 15.0 KiB/244.3 KiB (99.3 KiB/s) with 13 file(s) remaining\rCompleted 15.2 KiB/244.3 KiB (95.3 KiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/curation_notes.txt\nCompleted 15.2 KiB/244.3 KiB (95.3 KiB/s) with 12 file(s) remaining\rCompleted 29.2 KiB/244.3 KiB (176.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000417.vcml to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417.vcml\nCompleted 29.2 KiB/244.3 KiB (176.7 KiB/s) with 11 file(s) remaining\rCompleted 38.2 KiB/244.3 KiB (216.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000417_url.sedml to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417_url.sedml\nCompleted 38.2 KiB/244.3 KiB (216.0 KiB/s) with 10 file(s) remaining\rCompleted 42.8 KiB/244.3 KiB (238.9 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000417-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417-biopax2.owl\nCompleted 42.8 KiB/244.3 KiB (238.9 KiB/s) with 9 file(s) remaining\rCompleted 55.0 KiB/244.3 KiB (300.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000417_url.xml to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417_url.xml\nCompleted 55.0 KiB/244.3 KiB (300.0 KiB/s) with 8 file(s) remaining\rCompleted 58.3 KiB/244.3 KiB (311.4 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000417.svg to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417.svg\nCompleted 58.3 KiB/244.3 KiB (311.4 KiB/s) with 7 file(s) remaining\rCompleted 60.3 KiB/244.3 KiB (289.3 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/manifest.xml\nCompleted 60.3 KiB/244.3 KiB (289.3 KiB/s) with 6 file(s) remaining\rCompleted 65.3 KiB/244.3 KiB (295.6 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000417.png to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417.png\nCompleted 65.3 KiB/244.3 KiB (295.6 KiB/s) with 5 file(s) remaining\rCompleted 68.8 KiB/244.3 KiB (302.0 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000417.m to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417.m\nCompleted 68.8 KiB/244.3 KiB (302.0 KiB/s) with 4 file(s) remaining\rCompleted 90.9 KiB/244.3 KiB (394.2 KiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/curation_image.png\nCompleted 90.9 KiB/244.3 KiB (394.2 KiB/s) with 3 file(s) remaining\rCompleted 95.4 KiB/244.3 KiB (383.8 KiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/metadata.rdf\nCompleted 95.4 KiB/244.3 KiB (383.8 KiB/s) with 2 file(s) remaining\rCompleted 97.1 KiB/244.3 KiB (349.0 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000417.ode to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417.ode\nCompleted 97.1 KiB/244.3 KiB (349.0 KiB/s) with 1 file(s) remaining\rCompleted 244.3 KiB/244.3 KiB (816.9 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000417.pdf to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/contents/BIOMD0000000417.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (83.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b2577b6669655060d0d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000417_url.sedml\ncreating dataset /BIOMD0000000417_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-4de486e1-e4584076-dc86-b7f6f8-0598b2, chunk_size: (2, 1001)\ncreating dataset /BIOMD0000000417_url.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\ndataset created, uuid: d-4de486e1-e4584076-e082-577445-5eee59, chunk_size: (16, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000417_url.sedml\ncreating attribute uri in /BIOMD0000000417_url.sedml\ncreating attribute _type in /BIOMD0000000417_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000417_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000417_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000417_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000417_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000417_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000417_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000417_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000417_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000417_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000417_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000417_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000417_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000417_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000417_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000417_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000417_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000417_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000417_url.sedml\ncreate_links: /BIOMD0000000417_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000417_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000417_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\niterating over chunks for /BIOMD0000000417_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000417_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000417_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000417_url.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\niterating over chunks for /BIOMD0000000417_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000417_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b2577b6669655060d0d\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":1.161281,"sedDocuments":[{"location":"BIOMD0000000417_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  BIOMD0000000417_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 16 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000417_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":0.765018,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.127733,"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":0.167881,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Target","status":"SUCCEEDED"},{"id":"autogen_task1_Kd","status":"SUCCEEDED"},{"id":"autogen_task1_Ksp","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_dspksp","status":"SUCCEEDED"},{"id":"autogen_task1_dspspkd","status":"SUCCEEDED"},{"id":"autogen_task1_h","status":"SUCCEEDED"},{"id":"autogen_task1_k0","status":"SUCCEEDED"},{"id":"autogen_task1_ka","status":"SUCCEEDED"},{"id":"autogen_task1_ks","status":"SUCCEEDED"},{"id":"autogen_task1_ku","status":"SUCCEEDED"},{"id":"autogen_task1_s","status":"SUCCEEDED"},{"id":"autogen_task1_univ","status":"SUCCEEDED"},{"id":"autogen_task1____r1","status":"SUCCEEDED"},{"id":"autogen_task1____r2","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.366866,"curves":[{"id":"autogen_curve_task1_Target","status":"SUCCEEDED"}]}]}]}