{"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    423      0 --:--:-- --:--:-- --:--:--   423\n\r100  177k  100  177k    0     0   391k      0 --:--:-- --:--:-- --:--:--  391k\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 (17.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/rawLog.txt\nCompleted 3.1 KiB/3.1 KiB (46.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/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/BIOMD0000000184_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000184_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 19%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 116.2 KiB/116.2 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/outputs/reports.h5\nCompleted 101.9 KiB/118.3 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/output.zip\nCompleted 101.9 KiB/118.3 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 107.4 KiB/118.3 KiB (942.1 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/outputs/plots.zip\nCompleted 107.4 KiB/118.3 KiB (942.1 KiB/s) with 2 file(s) remaining\rCompleted 110.1 KiB/118.3 KiB (705.4 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/rawLog.txt\nCompleted 110.1 KiB/118.3 KiB (705.4 KiB/s) with 1 file(s) remaining\rCompleted 118.3 KiB/118.3 KiB (680.6 KiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000184_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/outputs/BIOMD0000000184_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/BIOMD0000000184-biopax2.owl  \n  inflating: contents/BIOMD0000000184-biopax3.owl  \n  inflating: contents/BIOMD0000000184-matlab.m  \n  inflating: contents/BIOMD0000000184-octave.m  \n  inflating: contents/BIOMD0000000184.m  \n  inflating: contents/BIOMD0000000184.ode  \n  inflating: contents/BIOMD0000000184.pdf  \n  inflating: contents/BIOMD0000000184.png  \n  inflating: contents/BIOMD0000000184.svg  \n  inflating: contents/BIOMD0000000184_url.sedml  \n  inflating: contents/BIOMD0000000184_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 17.0 KiB/304.8 KiB (193.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000184-biopax3.owl to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184-biopax3.owl\nCompleted 17.0 KiB/304.8 KiB (193.0 KiB/s) with 14 file(s) remaining\rCompleted 21.5 KiB/304.8 KiB (180.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000184-matlab.m to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184-matlab.m\nCompleted 21.5 KiB/304.8 KiB (180.7 KiB/s) with 13 file(s) remaining\rCompleted 34.4 KiB/304.8 KiB (263.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000184-biopax2.owl to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184-biopax2.owl\nCompleted 34.4 KiB/304.8 KiB (263.9 KiB/s) with 12 file(s) remaining\rCompleted 38.9 KiB/304.8 KiB (287.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000184-octave.m to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184-octave.m\nCompleted 38.9 KiB/304.8 KiB (287.0 KiB/s) with 11 file(s) remaining\rCompleted 51.0 KiB/304.8 KiB (362.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000184.svg to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184.svg\nCompleted 51.0 KiB/304.8 KiB (362.8 KiB/s) with 10 file(s) remaining\rCompleted 53.6 KiB/304.8 KiB (373.5 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/metadata.rdf\nCompleted 53.6 KiB/304.8 KiB (373.5 KiB/s) with 9 file(s) remaining\rCompleted 72.8 KiB/304.8 KiB (426.5 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000184_url.xml to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184_url.xml\nCompleted 72.8 KiB/304.8 KiB (426.5 KiB/s) with 8 file(s) remaining\rCompleted 86.9 KiB/304.8 KiB (428.7 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/curation_image.jpeg\nCompleted 86.9 KiB/304.8 KiB (428.7 KiB/s) with 7 file(s) remaining\rCompleted 101.2 KiB/304.8 KiB (493.4 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000184_url.sedml to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184_url.sedml\nCompleted 101.2 KiB/304.8 KiB (493.4 KiB/s) with 6 file(s) remaining\rCompleted 103.6 KiB/304.8 KiB (499.6 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000184.ode to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184.ode\nCompleted 103.6 KiB/304.8 KiB (499.6 KiB/s) with 5 file(s) remaining\rCompleted 103.7 KiB/304.8 KiB (494.4 KiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/curation_notes.txt\nCompleted 103.7 KiB/304.8 KiB (494.4 KiB/s) with 4 file(s) remaining\rCompleted 142.8 KiB/304.8 KiB (673.8 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000184.png to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184.png\nCompleted 142.8 KiB/304.8 KiB (673.8 KiB/s) with 3 file(s) remaining\rCompleted 147.3 KiB/304.8 KiB (687.7 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000184.m to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184.m\nCompleted 147.3 KiB/304.8 KiB (687.7 KiB/s) with 2 file(s) remaining\rCompleted 303.1 KiB/304.8 KiB (1.4 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000184.pdf to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/BIOMD0000000184.pdf\nCompleted 303.1 KiB/304.8 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 304.8 KiB/304.8 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (134.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109539a62a8be53f77b12/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000184_url.sedml\ncreating dataset /BIOMD0000000184_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-a10d762d-dea3e316-0bf3-91df5a-1dcc9d, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000184_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-a10d762d-dea3e316-e7a2-76ff44-fe80f7, chunk_size: (27, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000184_url.sedml\ncreating attribute uri in /BIOMD0000000184_url.sedml\ncreating attribute _type in /BIOMD0000000184_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000184_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000184_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000184_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000184_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000184_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000184_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000184_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000184_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000184_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000184_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000184_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000184_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000184_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000184_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000184_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000184_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000184_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000184_url.sedml\ncreate_links: /BIOMD0000000184_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000184_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000184_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000184_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000184_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000184_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000184_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /BIOMD0000000184_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000184_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647109539a62a8be53f77b12\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":1.463195,"sedDocuments":[{"location":"BIOMD0000000184_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  BIOMD0000000184_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: BIOMD0000000184_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":0.991462,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.165412,"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":0.259159,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_Z","status":"SUCCEEDED"},{"id":"autogen_task1_vin","status":"SUCCEEDED"},{"id":"autogen_task1_kout","status":"SUCCEEDED"},{"id":"autogen_task1_vM3","status":"SUCCEEDED"},{"id":"autogen_task1_k_CaA","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_k_CaI","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_kip3","status":"SUCCEEDED"},{"id":"autogen_task1_vM2","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_kf","status":"SUCCEEDED"},{"id":"autogen_task1_vp","status":"SUCCEEDED"},{"id":"autogen_task1_kp","status":"SUCCEEDED"},{"id":"autogen_task1_kdeg","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_ER","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_task1_R7","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.43653,"curves":[{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z","status":"SUCCEEDED"}]}]}]}