{"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    439      0 --:--:-- --:--:-- --:--:--   439\n\r100 65902  100 65902    0     0   152k      0 --:--:-- --:--:-- --:--:--  152k\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 (21.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/rawLog.txt\nCompleted 3.6 KiB/3.6 KiB (53.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/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/reports.h5 (deflated 14%)\n  adding: outputs/BIOMD0000000641_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000641_url.sedml/autogen_plot_for_task1.pdf (deflated 23%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 163.5 KiB/163.5 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/outputs/reports.h5\nCompleted 155.1 KiB/186.1 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/output.zip\nCompleted 155.1 KiB/186.1 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 167.3 KiB/186.1 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/outputs/plots.zip\nCompleted 167.3 KiB/186.1 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 169.9 KiB/186.1 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/rawLog.txt\nCompleted 169.9 KiB/186.1 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 186.1 KiB/186.1 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000641_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/outputs/BIOMD0000000641_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/BIOMD0000000641-biopax2.owl  \n  inflating: contents/BIOMD0000000641-biopax3.owl  \n  inflating: contents/BIOMD0000000641-matlab.m  \n  inflating: contents/BIOMD0000000641-octave.m  \n  inflating: contents/BIOMD0000000641.m  \n  inflating: contents/BIOMD0000000641.ode  \n  inflating: contents/BIOMD0000000641.png  \n  inflating: contents/BIOMD0000000641.sci  \n  inflating: contents/BIOMD0000000641.svg  \n  inflating: contents/BIOMD0000000641_url.sedml  \n  inflating: contents/BIOMD0000000641_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 6.9 KiB/153.5 KiB (98.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000641-biopax2.owl to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641-biopax2.owl\nCompleted 6.9 KiB/153.5 KiB (98.0 KiB/s) with 14 file(s) remaining\rCompleted 7.2 KiB/153.5 KiB (62.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000641.sci to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641.sci\nCompleted 7.2 KiB/153.5 KiB (62.1 KiB/s) with 13 file(s) remaining\rCompleted 12.2 KiB/153.5 KiB (100.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000641-matlab.m to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641-matlab.m\nCompleted 12.2 KiB/153.5 KiB (100.1 KiB/s) with 12 file(s) remaining\rCompleted 17.1 KiB/153.5 KiB (139.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000641-octave.m to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641-octave.m\nCompleted 17.1 KiB/153.5 KiB (139.5 KiB/s) with 11 file(s) remaining\rCompleted 17.9 KiB/153.5 KiB (132.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000641.svg to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641.svg\nCompleted 17.9 KiB/153.5 KiB (132.0 KiB/s) with 10 file(s) remaining\rCompleted 60.3 KiB/153.5 KiB (415.4 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000641_url.xml to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641_url.xml\nCompleted 60.3 KiB/153.5 KiB (415.4 KiB/s) with 9 file(s) remaining\rCompleted 74.9 KiB/153.5 KiB (471.2 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000641_url.sedml to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641_url.sedml\nCompleted 74.9 KiB/153.5 KiB (471.2 KiB/s) with 8 file(s) remaining\rCompleted 79.9 KiB/153.5 KiB (434.4 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000641.m to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641.m\nCompleted 79.9 KiB/153.5 KiB (434.4 KiB/s) with 7 file(s) remaining\rCompleted 84.2 KiB/153.5 KiB (435.9 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000641.png to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641.png\nCompleted 84.2 KiB/153.5 KiB (435.9 KiB/s) with 6 file(s) remaining\rCompleted 92.3 KiB/153.5 KiB (469.6 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000641-biopax3.owl to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641-biopax3.owl\nCompleted 92.3 KiB/153.5 KiB (469.6 KiB/s) with 5 file(s) remaining\rCompleted 144.3 KiB/153.5 KiB (719.1 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/curation_image.jpeg\nCompleted 144.3 KiB/153.5 KiB (719.1 KiB/s) with 4 file(s) remaining\rCompleted 148.7 KiB/153.5 KiB (736.4 KiB/s) with 4 file(s) remaining\rCompleted 148.9 KiB/153.5 KiB (732.8 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/metadata.rdf\nCompleted 148.9 KiB/153.5 KiB (732.8 KiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/curation_notes.txt\nCompleted 148.9 KiB/153.5 KiB (732.8 KiB/s) with 2 file(s) remaining\rCompleted 151.8 KiB/153.5 KiB (736.7 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000641.ode to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/BIOMD0000000641.ode\nCompleted 151.8 KiB/153.5 KiB (736.7 KiB/s) with 1 file(s) remaining\rCompleted 153.5 KiB/153.5 KiB (741.1 KiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (120.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711ba049c0d898ffdf150a/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000641_url.sedml\ncreating dataset /BIOMD0000000641_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\ndataset created, uuid: d-15c5a3f1-9d24fa74-0590-15bedd-b402f3, chunk_size: (13, 1001)\ncreating dataset /BIOMD0000000641_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\ndataset created, uuid: d-15c5a3f1-9d24fa74-2b92-677058-41b80e, chunk_size: (23, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000641_url.sedml\ncreating attribute uri in /BIOMD0000000641_url.sedml\ncreating attribute _type in /BIOMD0000000641_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000641_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000641_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000641_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000641_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000641_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000641_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000641_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000641_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000641_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000641_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000641_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000641_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000641_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000641_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000641_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000641_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000641_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000641_url.sedml\ncreate_links: /BIOMD0000000641_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000641_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000641_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\niterating over chunks for /BIOMD0000000641_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000641_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000641_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000641_url.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\niterating over chunks for /BIOMD0000000641_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 23, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000641_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711ba049c0d898ffdf150a\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.\nProcess 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 and upload the outputs of the simulation run ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":21.914534,"sedDocuments":[{"location":"BIOMD0000000641_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  BIOMD0000000641_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 23 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000641_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":21.600381,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":20.669816,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.229943,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Timeract","status":"SUCCEEDED"},{"id":"autogen_task1_Timerinact","status":"SUCCEEDED"},{"id":"autogen_task1_CellCact","status":"SUCCEEDED"},{"id":"autogen_task1_CellCina","status":"SUCCEEDED"},{"id":"autogen_task1_Effectoract","status":"SUCCEEDED"},{"id":"autogen_task1_Effectorina","status":"SUCCEEDED"},{"id":"autogen_task1_Damage","status":"SUCCEEDED"},{"id":"autogen_task1_HR","status":"SUCCEEDED"},{"id":"autogen_task1_NHEJ","status":"SUCCEEDED"},{"id":"autogen_task1_CellCycletot","status":"SUCCEEDED"},{"id":"autogen_task1_Effectortot","status":"SUCCEEDED"},{"id":"autogen_task1_Timertot","status":"SUCCEEDED"},{"id":"autogen_task1_Kd2t","status":"SUCCEEDED"},{"id":"autogen_task1_Kti2t","status":"SUCCEEDED"},{"id":"autogen_task1_Kcc2ch","status":"SUCCEEDED"},{"id":"autogen_task1_Kt2cc","status":"SUCCEEDED"},{"id":"autogen_task1_Kcc2a","status":"SUCCEEDED"},{"id":"autogen_task1_Kd2ch","status":"SUCCEEDED"},{"id":"autogen_task1_Kch2cc","status":"SUCCEEDED"},{"id":"autogen_task1_Km1","status":"SUCCEEDED"},{"id":"autogen_task1_Km10","status":"SUCCEEDED"},{"id":"autogen_task1_nucleus","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.566882,"curves":[{"id":"autogen_curve_task1_Timeract","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Timerinact","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CellCact","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CellCina","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Effectoract","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Effectorina","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Damage","status":"SUCCEEDED"},{"id":"autogen_curve_task1_HR","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NHEJ","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CellCycletot","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Effectortot","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Timertot","status":"SUCCEEDED"}]}]}]}