{"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    423      0 --:--:-- --:--:-- --:--:--   423\n\r100  436k  100  436k    0     0   973k      0 --:--:-- --:--:-- --:--:--  973k\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 (24.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/rawLog.txt\nCompleted 2.2 KiB/2.2 KiB (35.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 70%)\n  adding: outputs/Radosavljevic2009.sedml/ (stored 0%)\n  adding: outputs/Radosavljevic2009.sedml/plot_1_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 80%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 27.8 KiB/27.8 KiB (355.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/outputs/reports.h5\nCompleted 17.4 KiB/42.6 KiB (226.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/output.zip\nCompleted 17.4 KiB/42.6 KiB (226.2 KiB/s) with 3 file(s) remaining\rCompleted 26.6 KiB/42.6 KiB (207.4 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/outputs/plots.zip\nCompleted 26.6 KiB/42.6 KiB (207.4 KiB/s) with 2 file(s) remaining\rCompleted 29.2 KiB/42.6 KiB (219.8 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/rawLog.txt\nCompleted 29.2 KiB/42.6 KiB (219.8 KiB/s) with 1 file(s) remaining\rCompleted 42.6 KiB/42.6 KiB (210.8 KiB/s) with 1 file(s) remaining\rupload: outputs/Radosavljevic2009.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/outputs/Radosavljevic2009.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nsrun: Job 6617994 step creation temporarily disabled, retrying\nsrun: Step created for job 6617994\nArchive:  archive.omex\n  inflating: contents/MODEL1203070000-biopax2.owl  \n  inflating: contents/MODEL1203070000-biopax3.owl  \n  inflating: contents/MODEL1203070000-matlab.m  \n  inflating: contents/MODEL1203070000-octave.m  \n  inflating: contents/MODEL1203070000.m  \n  inflating: contents/MODEL1203070000.ode  \n  inflating: contents/MODEL1203070000.pdf  \n  inflating: contents/MODEL1203070000.png  \n  inflating: contents/MODEL1203070000.sci  \n  inflating: contents/MODEL1203070000.svg  \n  inflating: contents/MODEL1203070000_url.xml  \n  inflating: contents/Radosavljevic2009-biopax2.owl  \n  inflating: contents/Radosavljevic2009-biopax3.owl  \n  inflating: contents/Radosavljevic2009-matlab.m  \n  inflating: contents/Radosavljevic2009-octave.m  \n  inflating: contents/Radosavljevic2009.cps  \n  inflating: contents/Radosavljevic2009.ode  \n  inflating: contents/Radosavljevic2009.sedml  \n  inflating: contents/Radosavljevic2009.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 3.0 KiB/578.2 KiB (41.8 KiB/s) with 23 file(s) remaining\rupload: contents/MODEL1203070000-biopax2.owl to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000-biopax2.owl\nCompleted 3.0 KiB/578.2 KiB (41.8 KiB/s) with 22 file(s) remaining\rCompleted 5.9 KiB/578.2 KiB (45.3 KiB/s) with 22 file(s) remaining\rupload: contents/MODEL1203070000-matlab.m to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000-matlab.m\nCompleted 5.9 KiB/578.2 KiB (45.3 KiB/s) with 21 file(s) remaining\rCompleted 8.8 KiB/578.2 KiB (66.8 KiB/s) with 21 file(s) remaining\rupload: contents/Radosavljevic2009-matlab.m to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/Radosavljevic2009-matlab.m\nCompleted 8.8 KiB/578.2 KiB (66.8 KiB/s) with 20 file(s) remaining\rCompleted 9.7 KiB/578.2 KiB (62.7 KiB/s) with 20 file(s) remaining\rupload: contents/MODEL1203070000.svg to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000.svg\nCompleted 9.7 KiB/578.2 KiB (62.7 KiB/s) with 19 file(s) remaining\rCompleted 14.7 KiB/578.2 KiB (94.0 KiB/s) with 19 file(s) remaining\rupload: contents/MODEL1203070000.png to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000.png\nCompleted 14.7 KiB/578.2 KiB (94.0 KiB/s) with 18 file(s) remaining\rCompleted 15.6 KiB/578.2 KiB (98.6 KiB/s) with 18 file(s) remaining\rupload: contents/MODEL1203070000.sci to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000.sci\nCompleted 15.6 KiB/578.2 KiB (98.6 KiB/s) with 17 file(s) remaining\rCompleted 19.4 KiB/578.2 KiB (114.3 KiB/s) with 17 file(s) remaining\rupload: contents/Radosavljevic2009-biopax2.owl to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/Radosavljevic2009-biopax2.owl\nCompleted 19.4 KiB/578.2 KiB (114.3 KiB/s) with 16 file(s) remaining\rCompleted 23.5 KiB/578.2 KiB (130.7 KiB/s) with 16 file(s) remaining\rupload: contents/Radosavljevic2009-biopax3.owl to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/Radosavljevic2009-biopax3.owl\nCompleted 23.5 KiB/578.2 KiB (130.7 KiB/s) with 15 file(s) remaining\rCompleted 29.1 KiB/578.2 KiB (153.3 KiB/s) with 15 file(s) remaining\rupload: contents/MODEL1203070000_url.xml to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000_url.xml\nCompleted 29.1 KiB/578.2 KiB (153.3 KiB/s) with 14 file(s) remaining\rCompleted 31.9 KiB/578.2 KiB (163.8 KiB/s) with 14 file(s) remaining\rupload: contents/MODEL1203070000-octave.m to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000-octave.m\nCompleted 31.9 KiB/578.2 KiB (163.8 KiB/s) with 13 file(s) remaining\rCompleted 287.9 KiB/578.2 KiB (1.4 MiB/s) with 13 file(s) remaining \rCompleted 323.6 KiB/578.2 KiB (1.6 MiB/s) with 13 file(s) remaining \rupload: contents/Radosavljevic2009.cps to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/Radosavljevic2009.cps\nCompleted 323.6 KiB/578.2 KiB (1.6 MiB/s) with 12 file(s) remaining\rCompleted 326.5 KiB/578.2 KiB (1.6 MiB/s) with 12 file(s) remaining\rupload: contents/Radosavljevic2009-octave.m to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/Radosavljevic2009-octave.m\nCompleted 326.5 KiB/578.2 KiB (1.6 MiB/s) with 11 file(s) remaining\rCompleted 340.5 KiB/578.2 KiB (1.4 MiB/s) with 11 file(s) remaining\rupload: contents/Radosavljevic2009.xml to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/Radosavljevic2009.xml\nCompleted 340.5 KiB/578.2 KiB (1.4 MiB/s) with 10 file(s) remaining\rCompleted 341.1 KiB/578.2 KiB (1.4 MiB/s) with 10 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/curation_notes.txt\nCompleted 341.1 KiB/578.2 KiB (1.4 MiB/s) with 9 file(s) remaining\rCompleted 423.7 KiB/578.2 KiB (1.7 MiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/curation_image.png\nCompleted 423.7 KiB/578.2 KiB (1.7 MiB/s) with 8 file(s) remaining\rCompleted 427.3 KiB/578.2 KiB (1.7 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/metadata.rdf\nCompleted 427.3 KiB/578.2 KiB (1.7 MiB/s) with 7 file(s) remaining\rCompleted 430.0 KiB/578.2 KiB (1.6 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/manifest.xml\nCompleted 430.0 KiB/578.2 KiB (1.6 MiB/s) with 6 file(s) remaining\rCompleted 431.2 KiB/578.2 KiB (1.6 MiB/s) with 6 file(s) remaining\rupload: contents/Radosavljevic2009.ode to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/Radosavljevic2009.ode\nCompleted 431.2 KiB/578.2 KiB (1.6 MiB/s) with 5 file(s) remaining\rCompleted 433.3 KiB/578.2 KiB (1.6 MiB/s) with 5 file(s) remaining\rupload: contents/MODEL1203070000.m to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000.m\nCompleted 433.3 KiB/578.2 KiB (1.6 MiB/s) with 4 file(s) remaining\rCompleted 436.6 KiB/578.2 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: contents/MODEL1203070000-biopax3.owl to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000-biopax3.owl\nCompleted 436.6 KiB/578.2 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 443.0 KiB/578.2 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/Radosavljevic2009.sedml to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/Radosavljevic2009.sedml\nCompleted 443.0 KiB/578.2 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 444.1 KiB/578.2 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: contents/MODEL1203070000.ode to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000.ode\nCompleted 444.1 KiB/578.2 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 578.2 KiB/578.2 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: contents/MODEL1203070000.pdf to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/contents/MODEL1203070000.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 11.2 KiB/11.2 KiB (82.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711dc79a62a8be53f90bce/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Radosavljevic2009.sedml\ncreating dataset /Radosavljevic2009.sedml/autogen_report_for_task1, shape: (9, 101), type: float64\ndataset created, uuid: d-60a4a5e9-e0bfb5f2-59b1-81737b-a5e1d2, chunk_size: (9, 101)\ncreating dataset /Radosavljevic2009.sedml/plot_1_task1, shape: (3, 101), type: float64\ndataset created, uuid: d-60a4a5e9-e0bfb5f2-5945-162dec-14a9f3, chunk_size: (3, 101)\ncreating attribute combineArchiveLocation in /Radosavljevic2009.sedml\ncreating attribute uri in /Radosavljevic2009.sedml\ncreating attribute _type in /Radosavljevic2009.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Radosavljevic2009.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Radosavljevic2009.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Radosavljevic2009.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Radosavljevic2009.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Radosavljevic2009.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Radosavljevic2009.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Radosavljevic2009.sedml/autogen_report_for_task1\ncreating attribute uri in /Radosavljevic2009.sedml/autogen_report_for_task1\ncreating attribute _type in /Radosavljevic2009.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Radosavljevic2009.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Radosavljevic2009.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Radosavljevic2009.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Radosavljevic2009.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Radosavljevic2009.sedml/plot_1_task1\ncreating attribute sedmlId in /Radosavljevic2009.sedml/plot_1_task1\ncreating attribute sedmlName in /Radosavljevic2009.sedml/plot_1_task1\ncreating attribute uri in /Radosavljevic2009.sedml/plot_1_task1\ncreate_links: /\ngot link: Radosavljevic2009.sedml\ncreate_links: /Radosavljevic2009.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Radosavljevic2009.sedml/autogen_report_for_task1 to tgt: /Radosavljevic2009.sedml/autogen_report_for_task1, shape: (9, 101), type: float64\niterating over chunks for /Radosavljevic2009.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 101, 1))\ndone with dataload for /Radosavljevic2009.sedml/autogen_report_for_task1\nwrite_dataset src: /Radosavljevic2009.sedml/plot_1_task1 to tgt: /Radosavljevic2009.sedml/plot_1_task1, shape: (3, 101), type: float64\niterating over chunks for /Radosavljevic2009.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 101, 1))\ndone with dataload for /Radosavljevic2009.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711dc79a62a8be53f90bce\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.\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.\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":22.916981,"sedDocuments":[{"location":"Radosavljevic2009.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  Radosavljevic2009.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 9 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Radosavljevic2009.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":22.509254,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":21.983253,"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":0.336834,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.085045,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"}]}]}]}