{"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    411      0 --:--:-- --:--:-- --:--:--   412\n\r100  172k  100  172k    0     0   378k      0 --:--:-- --:--:-- --:--:--  378k\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 (21.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/rawLog.txt\nCompleted 4.2 KiB/4.2 KiB (58.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/BIOMD0000000266_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000266_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 17%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 160.3 KiB/160.3 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/outputs/reports.h5\nCompleted 141.0 KiB/158.2 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/output.zip\nCompleted 141.0 KiB/158.2 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 143.6 KiB/158.2 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/rawLog.txt\nCompleted 143.6 KiB/158.2 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 152.4 KiB/158.2 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000266_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/outputs/BIOMD0000000266_url.sedml/autogen_plot_for_task1.pdf\nCompleted 152.4 KiB/158.2 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 158.2 KiB/158.2 KiB (984.8 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000266-biopax2.owl  \n  inflating: contents/BIOMD0000000266-biopax3.owl  \n  inflating: contents/BIOMD0000000266-matlab.m  \n  inflating: contents/BIOMD0000000266-octave.m  \n  inflating: contents/BIOMD0000000266.m  \n  inflating: contents/BIOMD0000000266.ode  \n  inflating: contents/BIOMD0000000266.pdf  \n  inflating: contents/BIOMD0000000266.png  \n  inflating: contents/BIOMD0000000266.svg  \n  inflating: contents/BIOMD0000000266_url.sedml  \n  inflating: contents/BIOMD0000000266_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 8.1 KiB/~312.7 KiB (130.7 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000266-biopax2.owl to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266-biopax2.owl\nCompleted 8.1 KiB/~312.7 KiB (130.7 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 16.7 KiB/318.3 KiB (153.2 KiB/s) with 14 file(s) remaining                  \rupload: contents/BIOMD0000000266-matlab.m to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266-matlab.m\nCompleted 16.7 KiB/318.3 KiB (153.2 KiB/s) with 13 file(s) remaining\rCompleted 21.0 KiB/318.3 KiB (180.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000266.png to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266.png\nCompleted 21.0 KiB/318.3 KiB (180.6 KiB/s) with 12 file(s) remaining\rCompleted 29.9 KiB/318.3 KiB (254.4 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000266-biopax3.owl to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266-biopax3.owl\nCompleted 29.9 KiB/318.3 KiB (254.4 KiB/s) with 11 file(s) remaining\rCompleted 37.0 KiB/318.3 KiB (304.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000266.ode to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266.ode\nCompleted 37.0 KiB/318.3 KiB (304.0 KiB/s) with 10 file(s) remaining\rCompleted 37.8 KiB/318.3 KiB (277.3 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000266.svg to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266.svg\nCompleted 37.8 KiB/318.3 KiB (277.3 KiB/s) with 9 file(s) remaining\rCompleted 59.9 KiB/318.3 KiB (390.1 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000266_url.sedml to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266_url.sedml\nCompleted 59.9 KiB/318.3 KiB (390.1 KiB/s) with 8 file(s) remaining\rCompleted 60.3 KiB/318.3 KiB (351.7 KiB/s) with 8 file(s) remaining\rCompleted 68.9 KiB/318.3 KiB (396.3 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000266.m to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266.m\nCompleted 68.9 KiB/318.3 KiB (396.3 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/curation_notes.txt\nCompleted 68.9 KiB/318.3 KiB (396.3 KiB/s) with 6 file(s) remaining\rCompleted 110.7 KiB/318.3 KiB (622.3 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000266_url.xml to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266_url.xml\nCompleted 110.7 KiB/318.3 KiB (622.3 KiB/s) with 5 file(s) remaining\rCompleted 119.3 KiB/318.3 KiB (664.1 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000266-octave.m to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266-octave.m\nCompleted 119.3 KiB/318.3 KiB (664.1 KiB/s) with 4 file(s) remaining\rCompleted 143.5 KiB/318.3 KiB (788.6 KiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/curation_image.png\nCompleted 143.5 KiB/318.3 KiB (788.6 KiB/s) with 3 file(s) remaining\rCompleted 145.2 KiB/318.3 KiB (772.1 KiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/manifest.xml\nCompleted 145.2 KiB/318.3 KiB (772.1 KiB/s) with 2 file(s) remaining\rCompleted 312.7 KiB/318.3 KiB (1.6 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000266.pdf to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/BIOMD0000000266.pdf\nCompleted 312.7 KiB/318.3 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 318.3 KiB/318.3 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (127.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a729a62a8be53f79e3e/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000266_url.sedml\ncreating dataset /BIOMD0000000266_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-90bc39c9-df660696-2cef-6fe737-f6a012, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000266_url.sedml/autogen_report_for_task1, shape: (40, 1001), type: float64\ndataset created, uuid: d-90bc39c9-df660696-827e-f9922d-d0cea6, chunk_size: (40, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000266_url.sedml\ncreating attribute uri in /BIOMD0000000266_url.sedml\ncreating attribute _type in /BIOMD0000000266_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000266_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000266_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000266_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000266_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000266_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000266_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000266_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000266_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000266_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000266_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000266_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000266_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000266_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000266_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000266_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000266_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000266_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000266_url.sedml\ncreate_links: /BIOMD0000000266_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000266_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000266_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000266_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000266_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000266_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000266_url.sedml/autogen_report_for_task1, shape: (40, 1001), type: float64\niterating over chunks for /BIOMD0000000266_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 40, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000266_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710a729a62a8be53f79e3e\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.710294,"sedDocuments":[{"location":"BIOMD0000000266_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  BIOMD0000000266_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 40 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000266_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":1.250337,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.234216,"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":0.351878,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_X0","status":"SUCCEEDED"},{"id":"autogen_task1_X1","status":"SUCCEEDED"},{"id":"autogen_task1_X2","status":"SUCCEEDED"},{"id":"autogen_task1_X3","status":"SUCCEEDED"},{"id":"autogen_task1_X4","status":"SUCCEEDED"},{"id":"autogen_task1_X5","status":"SUCCEEDED"},{"id":"autogen_task1_X6","status":"SUCCEEDED"},{"id":"autogen_task1_X7","status":"SUCCEEDED"},{"id":"autogen_task1_heat_shock","status":"SUCCEEDED"},{"id":"autogen_task1_X8","status":"SUCCEEDED"},{"id":"autogen_task1_X9","status":"SUCCEEDED"},{"id":"autogen_task1_X10","status":"SUCCEEDED"},{"id":"autogen_task1_X11","status":"SUCCEEDED"},{"id":"autogen_task1_X12r","status":"SUCCEEDED"},{"id":"autogen_task1_X12f","status":"SUCCEEDED"},{"id":"autogen_task1_X13","status":"SUCCEEDED"},{"id":"autogen_task1_X14","status":"SUCCEEDED"},{"id":"autogen_task1_X15r","status":"SUCCEEDED"},{"id":"autogen_task1_X15f","status":"SUCCEEDED"},{"id":"autogen_task1_X16","status":"SUCCEEDED"},{"id":"autogen_task1_X17","status":"SUCCEEDED"},{"id":"autogen_task1_X18","status":"SUCCEEDED"},{"id":"autogen_task1_X19","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X1_in","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X1_out","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X2_in","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X2_out","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X3_in","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X3_out","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X4_in","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X4_out","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X5_in","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X5_out","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X6_in","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X6_out","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X7_in","status":"SUCCEEDED"},{"id":"autogen_task1_flux_X7_out","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_external","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.495047,"curves":[{"id":"autogen_curve_task1_X0","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X5","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X6","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X7","status":"SUCCEEDED"}]}]}]}