{"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    442      0 --:--:-- --:--:-- --:--:--   442\n\r100  199k  100  199k    0     0   435k      0 --:--:-- --:--:-- --:--:--  435k\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 (26.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (49.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/BIOMD0000000308_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000308_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 78%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 29.1 KiB/29.1 KiB (402.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/outputs/reports.h5\nCompleted 14.4 KiB/31.2 KiB (196.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/output.zip\nCompleted 14.4 KiB/31.2 KiB (196.6 KiB/s) with 3 file(s) remaining\rCompleted 20.0 KiB/31.2 KiB (194.4 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/outputs/plots.zip\nCompleted 20.0 KiB/31.2 KiB (194.4 KiB/s) with 2 file(s) remaining\rCompleted 28.6 KiB/31.2 KiB (235.2 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000308_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/outputs/BIOMD0000000308_url.sedml/autogen_plot_for_task1.pdf\nCompleted 28.6 KiB/31.2 KiB (235.2 KiB/s) with 1 file(s) remaining\rCompleted 31.2 KiB/31.2 KiB (221.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000308-biopax2.owl  \n  inflating: contents/BIOMD0000000308-biopax3.owl  \n  inflating: contents/BIOMD0000000308-matlab.m  \n  inflating: contents/BIOMD0000000308-octave.m  \n  inflating: contents/BIOMD0000000308.m  \n  inflating: contents/BIOMD0000000308.ode  \n  inflating: contents/BIOMD0000000308.pdf  \n  inflating: contents/BIOMD0000000308.png  \n  inflating: contents/BIOMD0000000308.svg  \n  inflating: contents/BIOMD0000000308.vcml  \n  inflating: contents/BIOMD0000000308_url.sedml  \n  inflating: contents/BIOMD0000000308_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 16.0 KiB/352.9 KiB (193.9 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000308-biopax3.owl to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308-biopax3.owl\nCompleted 16.0 KiB/352.9 KiB (193.9 KiB/s) with 15 file(s) remaining\rCompleted 27.7 KiB/352.9 KiB (234.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000308-biopax2.owl to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308-biopax2.owl\nCompleted 27.7 KiB/352.9 KiB (234.2 KiB/s) with 14 file(s) remaining\rCompleted 32.1 KiB/352.9 KiB (267.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000308-octave.m to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308-octave.m\nCompleted 32.1 KiB/352.9 KiB (267.0 KiB/s) with 13 file(s) remaining\rCompleted 36.5 KiB/352.9 KiB (278.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000308-matlab.m to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308-matlab.m\nCompleted 36.5 KiB/352.9 KiB (278.2 KiB/s) with 12 file(s) remaining\rCompleted 49.9 KiB/352.9 KiB (365.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000308.svg to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308.svg\nCompleted 49.9 KiB/352.9 KiB (365.7 KiB/s) with 11 file(s) remaining\rCompleted 50.3 KiB/352.9 KiB (342.4 KiB/s) with 11 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/curation_notes.txt\nCompleted 50.3 KiB/352.9 KiB (342.4 KiB/s) with 10 file(s) remaining\rCompleted 65.4 KiB/352.9 KiB (401.1 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000308_url.sedml to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308_url.sedml\nCompleted 65.4 KiB/352.9 KiB (401.1 KiB/s) with 9 file(s) remaining\rCompleted 86.7 KiB/352.9 KiB (499.4 KiB/s) with 9 file(s) remaining\rCompleted 90.1 KiB/352.9 KiB (512.9 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/metadata.rdf\nCompleted 90.1 KiB/352.9 KiB (512.9 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000308_url.xml to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308_url.xml\nCompleted 90.1 KiB/352.9 KiB (512.9 KiB/s) with 7 file(s) remaining\rCompleted 117.7 KiB/352.9 KiB (647.2 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000308.vcml to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308.vcml\nCompleted 117.7 KiB/352.9 KiB (647.2 KiB/s) with 6 file(s) remaining\rCompleted 137.5 KiB/352.9 KiB (733.3 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/curation_image.png\nCompleted 137.5 KiB/352.9 KiB (733.3 KiB/s) with 5 file(s) remaining\rCompleted 139.4 KiB/352.9 KiB (731.2 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/manifest.xml\nCompleted 139.4 KiB/352.9 KiB (731.2 KiB/s) with 4 file(s) remaining\rCompleted 179.2 KiB/352.9 KiB (907.5 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000308.png to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308.png\nCompleted 179.2 KiB/352.9 KiB (907.5 KiB/s) with 3 file(s) remaining\rCompleted 183.6 KiB/352.9 KiB (918.9 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000308.m to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308.m\nCompleted 183.6 KiB/352.9 KiB (918.9 KiB/s) with 2 file(s) remaining\rCompleted 350.5 KiB/352.9 KiB (1.7 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000308.pdf to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308.pdf\nCompleted 350.5 KiB/352.9 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 352.9 KiB/352.9 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000308.ode to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/contents/BIOMD0000000308.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (98.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710afe0dcacb55678ba737/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000308_url.sedml\ncreating dataset /BIOMD0000000308_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-e343c85b-275d6ef1-5a5a-0b95e1-aba716, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000308_url.sedml/autogen_report_for_task1, shape: (28, 1001), type: float64\ndataset created, uuid: d-e343c85b-275d6ef1-af23-4c265d-a5a7bd, chunk_size: (28, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000308_url.sedml\ncreating attribute uri in /BIOMD0000000308_url.sedml\ncreating attribute _type in /BIOMD0000000308_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000308_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000308_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000308_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000308_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000308_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000308_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000308_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000308_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000308_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000308_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000308_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000308_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000308_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000308_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000308_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000308_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000308_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000308_url.sedml\ncreate_links: /BIOMD0000000308_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000308_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000308_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000308_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000308_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000308_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000308_url.sedml/autogen_report_for_task1, shape: (28, 1001), type: float64\niterating over chunks for /BIOMD0000000308_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 28, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000308_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710afe0dcacb55678ba737\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 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.\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 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":1.437178,"sedDocuments":[{"location":"BIOMD0000000308_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  BIOMD0000000308_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 28 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000308_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":0.989135,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.155415,"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":0.259317,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Rp","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_Yp","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_k0","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k2_prime","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_Yt","status":"SUCCEEDED"},{"id":"autogen_task1_Km3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_Km4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_Rt","status":"SUCCEEDED"},{"id":"autogen_task1_Km5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_Km6","status":"SUCCEEDED"},{"id":"autogen_task1_env","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_task1_r5","status":"SUCCEEDED"},{"id":"autogen_task1_r6","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.442086,"curves":[{"id":"autogen_curve_task1_Rp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Yp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R","status":"SUCCEEDED"}]}]}]}