{"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    436      0 --:--:-- --:--:-- --:--:--   437\n\r100  170k  100  170k    0     0   386k      0 --:--:-- --:--:-- --:--:--  386k\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 (25.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/rawLog.txt\nCompleted 2.5 KiB/2.5 KiB (37.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/MODEL1006230019.sedml/ (stored 0%)\n  adding: outputs/MODEL1006230019.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 36%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 51.4 KiB/51.4 KiB (660.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/outputs/reports.h5\nCompleted 41.1 KiB/58.4 KiB (569.0 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/output.zip\nCompleted 41.1 KiB/58.4 KiB (569.0 KiB/s) with 3 file(s) remaining\rCompleted 46.9 KiB/58.4 KiB (461.8 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/outputs/plots.zip\nCompleted 46.9 KiB/58.4 KiB (461.8 KiB/s) with 2 file(s) remaining\rCompleted 49.5 KiB/58.4 KiB (449.0 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/rawLog.txt\nCompleted 49.5 KiB/58.4 KiB (449.0 KiB/s) with 1 file(s) remaining\rCompleted 58.4 KiB/58.4 KiB (373.0 KiB/s) with 1 file(s) remaining\rupload: outputs/MODEL1006230019.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/outputs/MODEL1006230019.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000672-biopax2.owl  \n  inflating: contents/BIOMD0000000672-biopax3.owl  \n  inflating: contents/BIOMD0000000672-matlab.m  \n  inflating: contents/BIOMD0000000672-octave.m  \n  inflating: contents/BIOMD0000000672.m  \n  inflating: contents/BIOMD0000000672.pdf  \n  inflating: contents/BIOMD0000000672.png  \n  inflating: contents/BIOMD0000000672.svg  \n  inflating: contents/BIOMD0000000672_url.xml  \n  inflating: contents/MODEL1006230019.cps  \n  inflating: contents/MODEL1006230019.sedml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 4.3 KiB/265.7 KiB (65.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000672-biopax3.owl to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/BIOMD0000000672-biopax3.owl\nCompleted 4.3 KiB/265.7 KiB (65.0 KiB/s) with 14 file(s) remaining\rCompleted 7.8 KiB/265.7 KiB (69.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000672-matlab.m to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/BIOMD0000000672-matlab.m\nCompleted 7.8 KiB/265.7 KiB (69.7 KiB/s) with 13 file(s) remaining\rCompleted 12.0 KiB/265.7 KiB (102.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000672-biopax2.owl to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/BIOMD0000000672-biopax2.owl\nCompleted 12.0 KiB/265.7 KiB (102.8 KiB/s) with 12 file(s) remaining\rCompleted 15.4 KiB/265.7 KiB (125.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000672-octave.m to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/BIOMD0000000672-octave.m\nCompleted 15.4 KiB/265.7 KiB (125.0 KiB/s) with 11 file(s) remaining\rCompleted 17.2 KiB/265.7 KiB (133.8 KiB/s) with 11 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/manifest.xml\nCompleted 17.2 KiB/265.7 KiB (133.8 KiB/s) with 10 file(s) remaining\rCompleted 51.9 KiB/265.7 KiB (395.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000672_url.xml to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/BIOMD0000000672_url.xml\nCompleted 51.9 KiB/265.7 KiB (395.6 KiB/s) with 9 file(s) remaining\rCompleted 61.5 KiB/265.7 KiB (387.4 KiB/s) with 9 file(s) remaining\rupload: contents/MODEL1006230019.sedml to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/MODEL1006230019.sedml\nCompleted 61.5 KiB/265.7 KiB (387.4 KiB/s) with 8 file(s) remaining\rCompleted 104.8 KiB/265.7 KiB (653.9 KiB/s) with 8 file(s) remaining\rupload: contents/MODEL1006230019.cps to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/MODEL1006230019.cps\nCompleted 104.8 KiB/265.7 KiB (653.9 KiB/s) with 7 file(s) remaining\rCompleted 109.1 KiB/265.7 KiB (645.5 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000672.png to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/BIOMD0000000672.png\nCompleted 109.1 KiB/265.7 KiB (645.5 KiB/s) with 6 file(s) remaining\rCompleted 121.3 KiB/265.7 KiB (708.4 KiB/s) with 6 file(s) remaining\rCompleted 122.1 KiB/265.7 KiB (706.3 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000672.svg to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/BIOMD0000000672.svg\nCompleted 122.1 KiB/265.7 KiB (706.3 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/curation_image.png\nCompleted 122.1 KiB/265.7 KiB (706.3 KiB/s) with 4 file(s) remaining\rCompleted 122.4 KiB/265.7 KiB (681.7 KiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/curation_notes.txt\nCompleted 122.4 KiB/265.7 KiB (681.7 KiB/s) with 3 file(s) remaining\rCompleted 125.8 KiB/265.7 KiB (690.7 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000672.m to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/BIOMD0000000672.m\nCompleted 125.8 KiB/265.7 KiB (690.7 KiB/s) with 2 file(s) remaining\rCompleted 130.7 KiB/265.7 KiB (643.6 KiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/metadata.rdf\nCompleted 130.7 KiB/265.7 KiB (643.6 KiB/s) with 1 file(s) remaining\rCompleted 265.7 KiB/265.7 KiB (1.1 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000672.pdf to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/contents/BIOMD0000000672.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.4 KiB/8.4 KiB (121.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c070dcacb55678cbeb3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /MODEL1006230019.sedml\ncreating dataset /MODEL1006230019.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\ndataset created, uuid: d-f80847ee-ca6da50a-237a-055d22-ef57ee, chunk_size: (16, 1001)\ncreating dataset /MODEL1006230019.sedml/plot_1_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-f80847ee-ca6da50a-9275-6b92be-fff43f, chunk_size: (2, 1001)\ncreating attribute combineArchiveLocation in /MODEL1006230019.sedml\ncreating attribute uri in /MODEL1006230019.sedml\ncreating attribute _type in /MODEL1006230019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1006230019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /MODEL1006230019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /MODEL1006230019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /MODEL1006230019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /MODEL1006230019.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /MODEL1006230019.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /MODEL1006230019.sedml/autogen_report_for_task1\ncreating attribute uri in /MODEL1006230019.sedml/autogen_report_for_task1\ncreating attribute _type in /MODEL1006230019.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1006230019.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /MODEL1006230019.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /MODEL1006230019.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /MODEL1006230019.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /MODEL1006230019.sedml/plot_1_task1\ncreating attribute sedmlId in /MODEL1006230019.sedml/plot_1_task1\ncreating attribute sedmlName in /MODEL1006230019.sedml/plot_1_task1\ncreating attribute uri in /MODEL1006230019.sedml/plot_1_task1\ncreate_links: /\ngot link: MODEL1006230019.sedml\ncreate_links: /MODEL1006230019.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /MODEL1006230019.sedml/autogen_report_for_task1 to tgt: /MODEL1006230019.sedml/autogen_report_for_task1, shape: (16, 1001), type: float64\niterating over chunks for /MODEL1006230019.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1006230019.sedml/autogen_report_for_task1\nwrite_dataset src: /MODEL1006230019.sedml/plot_1_task1 to tgt: /MODEL1006230019.sedml/plot_1_task1, shape: (2, 1001), type: float64\niterating over chunks for /MODEL1006230019.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1006230019.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c070dcacb55678cbeb3\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 and upload the outputs of the simulation run ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":19.898892,"sedDocuments":[{"location":"MODEL1006230019.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  MODEL1006230019.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      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: MODEL1006230019.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_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: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":19.60303,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":19.100723,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.219096,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.173231,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_H2","status":"SUCCEEDED"},{"id":"autogen_task1_H1","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_t_on","status":"SUCCEEDED"},{"id":"autogen_task1_t_off","status":"SUCCEEDED"},{"id":"autogen_task1_A_max","status":"SUCCEEDED"},{"id":"autogen_task1_beta_I","status":"SUCCEEDED"},{"id":"autogen_task1_beta_C","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_lamda","status":"SUCCEEDED"},{"id":"autogen_task1_tau_I","status":"SUCCEEDED"},{"id":"autogen_task1_tau_C","status":"SUCCEEDED"},{"id":"autogen_task1_tau_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_tau_lamda","status":"SUCCEEDED"},{"id":"autogen_task1_COMpartment","status":"SUCCEEDED"}]}]}]}