{"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  184k  100  184k    0     0   419k      0 --:--:-- --:--:-- --:--:--  419k\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 (22.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (46.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/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/BIOMD0000000277_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000277_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 38%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 60.3 KiB/60.3 KiB (731.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/outputs/reports.h5\nCompleted 45.1 KiB/61.2 KiB (552.7 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/output.zip\nCompleted 45.1 KiB/61.2 KiB (552.7 KiB/s) with 3 file(s) remaining\rCompleted 50.4 KiB/61.2 KiB (508.0 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/outputs/plots.zip\nCompleted 50.4 KiB/61.2 KiB (508.0 KiB/s) with 2 file(s) remaining\rCompleted 58.5 KiB/61.2 KiB (508.3 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000277_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/outputs/BIOMD0000000277_url.sedml/autogen_plot_for_task1.pdf\nCompleted 58.5 KiB/61.2 KiB (508.3 KiB/s) with 1 file(s) remaining\rCompleted 61.2 KiB/61.2 KiB (511.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000277-biopax2.owl  \n  inflating: contents/BIOMD0000000277-biopax3.owl  \n  inflating: contents/BIOMD0000000277-matlab.m  \n  inflating: contents/BIOMD0000000277-octave.m  \n  inflating: contents/BIOMD0000000277.m  \n  inflating: contents/BIOMD0000000277.ode  \n  inflating: contents/BIOMD0000000277.pdf  \n  inflating: contents/BIOMD0000000277.png  \n  inflating: contents/BIOMD0000000277.svg  \n  inflating: contents/BIOMD0000000277_url.sedml  \n  inflating: contents/BIOMD0000000277_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/~275.5 KiB (85.2 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000277-biopax2.owl to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277-biopax2.owl\nCompleted 5.7 KiB/~275.5 KiB (85.2 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 10.7 KiB/283.0 KiB (95.8 KiB/s) with 14 file(s) remaining                  \rupload: contents/BIOMD0000000277-octave.m to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277-octave.m\nCompleted 10.7 KiB/283.0 KiB (95.8 KiB/s) with 13 file(s) remaining\rCompleted 15.7 KiB/283.0 KiB (133.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000277.png to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277.png\nCompleted 15.7 KiB/283.0 KiB (133.5 KiB/s) with 12 file(s) remaining\rCompleted 20.7 KiB/283.0 KiB (173.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000277-matlab.m to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277-matlab.m\nCompleted 20.7 KiB/283.0 KiB (173.5 KiB/s) with 11 file(s) remaining\rCompleted 21.5 KiB/283.0 KiB (169.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000277.svg to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277.svg\nCompleted 21.5 KiB/283.0 KiB (169.3 KiB/s) with 10 file(s) remaining\rCompleted 23.3 KiB/283.0 KiB (162.8 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/manifest.xml\nCompleted 23.3 KiB/283.0 KiB (162.8 KiB/s) with 9 file(s) remaining\rCompleted 37.9 KiB/283.0 KiB (245.2 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000277_url.sedml to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277_url.sedml\nCompleted 37.9 KiB/283.0 KiB (245.2 KiB/s) with 8 file(s) remaining\rCompleted 60.4 KiB/283.0 KiB (366.3 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000277_url.xml to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277_url.xml\nCompleted 60.4 KiB/283.0 KiB (366.3 KiB/s) with 7 file(s) remaining\rCompleted 66.5 KiB/283.0 KiB (378.0 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000277-biopax3.owl to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277-biopax3.owl\nCompleted 66.5 KiB/283.0 KiB (378.0 KiB/s) with 6 file(s) remaining\rCompleted 71.5 KiB/283.0 KiB (396.6 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000277.m to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277.m\nCompleted 71.5 KiB/283.0 KiB (396.6 KiB/s) with 5 file(s) remaining\rCompleted 121.9 KiB/283.0 KiB (670.5 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/curation_image.png\nCompleted 121.9 KiB/283.0 KiB (670.5 KiB/s) with 4 file(s) remaining\rCompleted 129.4 KiB/283.0 KiB (701.7 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/metadata.rdf\nCompleted 129.4 KiB/283.0 KiB (701.7 KiB/s) with 3 file(s) remaining\rCompleted 132.5 KiB/283.0 KiB (700.7 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000277.ode to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277.ode\nCompleted 132.5 KiB/283.0 KiB (700.7 KiB/s) with 2 file(s) remaining\rCompleted 133.1 KiB/283.0 KiB (695.7 KiB/s) with 2 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/curation_notes.txt\nCompleted 133.1 KiB/283.0 KiB (695.7 KiB/s) with 1 file(s) remaining\rCompleted 283.0 KiB/283.0 KiB (1.4 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000277.pdf to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/contents/BIOMD0000000277.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (107.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a940dcacb55678b9af8/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000277_url.sedml\ncreating dataset /BIOMD0000000277_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-1e9ba615-c08277a3-5b16-8568e1-a67365, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000277_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-1e9ba615-c08277a3-564d-320772-5ac5d3, chunk_size: (27, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000277_url.sedml\ncreating attribute uri in /BIOMD0000000277_url.sedml\ncreating attribute _type in /BIOMD0000000277_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000277_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000277_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000277_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000277_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000277_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000277_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000277_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000277_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000277_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000277_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000277_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000277_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000277_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000277_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000277_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000277_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000277_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000277_url.sedml\ncreate_links: /BIOMD0000000277_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000277_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000277_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000277_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000277_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000277_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000277_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /BIOMD0000000277_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000277_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710a940dcacb55678b9af8\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":1.35401,"sedDocuments":[{"location":"BIOMD0000000277_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  BIOMD0000000277_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 27 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000277_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":0.953009,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.150742,"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":0.279974,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x1","status":"SUCCEEDED"},{"id":"autogen_task1_x2","status":"SUCCEEDED"},{"id":"autogen_task1_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_m_Ca","status":"SUCCEEDED"},{"id":"autogen_task1_m1","status":"SUCCEEDED"},{"id":"autogen_task1_m2","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_1","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_2","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_Ca0","status":"SUCCEEDED"},{"id":"autogen_task1_Ca1","status":"SUCCEEDED"},{"id":"autogen_task1_t0","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_x1_n","status":"SUCCEEDED"},{"id":"autogen_task1_x2_n","status":"SUCCEEDED"},{"id":"autogen_task1_x2_min","status":"SUCCEEDED"},{"id":"autogen_task1_x2_max","status":"SUCCEEDED"},{"id":"autogen_task1_Ca0_baseline","status":"SUCCEEDED"},{"id":"autogen_task1_PTG_pool","status":"SUCCEEDED"},{"id":"autogen_task1_Plasma_pool","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.400064,"curves":[{"id":"autogen_curve_task1_x1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca","status":"SUCCEEDED"}]}]}]}