{"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    427      0 --:--:-- --:--:-- --:--:--   427\n\r100  266k  100  266k    0     0   583k      0 --:--:-- --:--:-- --:--:--  583k\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 (25.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (59.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000012_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000012_url.sedml/autogen_plot_for_task1.pdf (deflated 26%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/reports.h5 (deflated 13%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 212.8 KiB/212.8 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/outputs/reports.h5\nCompleted 195.1 KiB/216.2 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/output.zip\nCompleted 195.1 KiB/216.2 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 202.8 KiB/216.2 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/outputs/plots.zip\nCompleted 202.8 KiB/216.2 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 205.5 KiB/216.2 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/rawLog.txt\nCompleted 205.5 KiB/216.2 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 216.2 KiB/216.2 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000012_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/outputs/BIOMD0000000012_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/BIOMD0000000012-biopax2.owl  \n  inflating: contents/BIOMD0000000012-biopax3.owl  \n  inflating: contents/BIOMD0000000012-matlab.m  \n  inflating: contents/BIOMD0000000012-octave.m  \n  inflating: contents/BIOMD0000000012.m  \n  inflating: contents/BIOMD0000000012.ode  \n  inflating: contents/BIOMD0000000012.pdf  \n  inflating: contents/BIOMD0000000012.png  \n  inflating: contents/BIOMD0000000012.svg  \n  inflating: contents/BIOMD0000000012.vcml  \n  inflating: contents/BIOMD0000000012_manual.png  \n  inflating: contents/BIOMD0000000012_manual.svg  \n  inflating: contents/BIOMD0000000012_url.sedml  \n  inflating: contents/BIOMD0000000012_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 5.6 KiB/548.1 KiB (45.5 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000012-matlab.m to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012-matlab.m\nCompleted 5.6 KiB/548.1 KiB (45.5 KiB/s) with 17 file(s) remaining\rCompleted 19.9 KiB/548.1 KiB (148.1 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000012-biopax2.owl to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012-biopax2.owl\nCompleted 19.9 KiB/548.1 KiB (148.1 KiB/s) with 16 file(s) remaining\rCompleted 58.0 KiB/548.1 KiB (407.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000012.png to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012.png\nCompleted 58.0 KiB/548.1 KiB (407.5 KiB/s) with 15 file(s) remaining\rCompleted 96.1 KiB/548.1 KiB (598.8 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000012_manual.png to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012_manual.png\nCompleted 96.1 KiB/548.1 KiB (598.8 KiB/s) with 14 file(s) remaining\rCompleted 153.9 KiB/548.1 KiB (932.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000012.vcml to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012.vcml\nCompleted 153.9 KiB/548.1 KiB (932.1 KiB/s) with 13 file(s) remaining\rCompleted 159.5 KiB/548.1 KiB (908.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000012-octave.m to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012-octave.m\nCompleted 159.5 KiB/548.1 KiB (908.9 KiB/s) with 12 file(s) remaining\rCompleted 194.4 KiB/548.1 KiB (1.1 MiB/s) with 12 file(s) remaining  \rupload: contents/BIOMD0000000012.svg to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012.svg\nCompleted 194.4 KiB/548.1 KiB (1.1 MiB/s) with 11 file(s) remaining\rCompleted 229.3 KiB/548.1 KiB (1.3 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000012_manual.svg to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012_manual.svg\nCompleted 229.3 KiB/548.1 KiB (1.3 MiB/s) with 10 file(s) remaining\rCompleted 237.2 KiB/548.1 KiB (1.3 MiB/s) with 10 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/curation_image.png\nCompleted 237.2 KiB/548.1 KiB (1.3 MiB/s) with 9 file(s) remaining\rCompleted 256.9 KiB/548.1 KiB (1.3 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000012_url.sedml to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012_url.sedml\nCompleted 256.9 KiB/548.1 KiB (1.3 MiB/s) with 8 file(s) remaining\rCompleted 257.2 KiB/548.1 KiB (1.3 MiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/curation_notes.txt\nCompleted 257.2 KiB/548.1 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 259.3 KiB/548.1 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/manifest.xml\nCompleted 259.3 KiB/548.1 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 304.4 KiB/548.1 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000012_url.xml to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012_url.xml\nCompleted 304.4 KiB/548.1 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 318.6 KiB/548.1 KiB (1.4 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/metadata.rdf\nCompleted 318.6 KiB/548.1 KiB (1.4 MiB/s) with 4 file(s) remaining\rCompleted 519.0 KiB/548.1 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000012.pdf to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012.pdf\nCompleted 519.0 KiB/548.1 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 523.8 KiB/548.1 KiB (2.1 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000012.m to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012.m\nCompleted 523.8 KiB/548.1 KiB (2.1 MiB/s) with 2 file(s) remaining\rCompleted 527.8 KiB/548.1 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000012.ode to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012.ode\nCompleted 527.8 KiB/548.1 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 548.1 KiB/548.1 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000012-biopax3.owl to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/contents/BIOMD0000000012-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.5 KiB/9.5 KiB (112.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471071749c0d898ffdd8e26/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000012_url.sedml\ncreating dataset /BIOMD0000000012_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-732a1520-f76e95ba-3e62-cb1673-bd0cad, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000012_url.sedml/autogen_report_for_task1, shape: (36, 1001), type: float64\ndataset created, uuid: d-732a1520-f76e95ba-0bf8-a0cac0-b92ebb, chunk_size: (36, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000012_url.sedml\ncreating attribute uri in /BIOMD0000000012_url.sedml\ncreating attribute _type in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000012_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000012_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000012_url.sedml\ncreate_links: /BIOMD0000000012_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000012_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000012_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000012_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000012_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000012_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000012_url.sedml/autogen_report_for_task1, shape: (36, 1001), type: float64\niterating over chunks for /BIOMD0000000012_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 36, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000012_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471071749c0d898ffdd8e26\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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 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 and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":21.171644,"sedDocuments":[{"location":"BIOMD0000000012_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  BIOMD0000000012_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 36 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000012_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":20.834113,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":20.08081,"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":0.314455,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_PX","status":"SUCCEEDED"},{"id":"autogen_task1_PY","status":"SUCCEEDED"},{"id":"autogen_task1_PZ","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_Z","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_alpha0","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_eff","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_KM","status":"SUCCEEDED"},{"id":"autogen_task1_tau_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_tau_prot","status":"SUCCEEDED"},{"id":"autogen_task1_t_ave","status":"SUCCEEDED"},{"id":"autogen_task1_kd_mRNA","status":"SUCCEEDED"},{"id":"autogen_task1_kd_prot","status":"SUCCEEDED"},{"id":"autogen_task1_k_tl","status":"SUCCEEDED"},{"id":"autogen_task1_a_tr","status":"SUCCEEDED"},{"id":"autogen_task1_ps_a","status":"SUCCEEDED"},{"id":"autogen_task1_ps_0","status":"SUCCEEDED"},{"id":"autogen_task1_a0_tr","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction1","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction2","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction3","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction4","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction5","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction6","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction7","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction8","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction9","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction10","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction11","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction12","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.306856,"curves":[{"id":"autogen_curve_task1_PX","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PY","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PZ","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z","status":"SUCCEEDED"}]}]}]}