{"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    446      0 --:--:-- --:--:-- --:--:--   448\n\r 47  167k   47 82060    0     0   192k      0 --:--:-- --:--:-- --:--:--  192k\r100  167k  100  167k    0     0   395k      0 --:--:-- --:--:-- --:--:-- 17.0M\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 (24.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/rawLog.txt\nCompleted 3.5 KiB/3.5 KiB (56.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000330_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000330_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/reports.h5 (deflated 26%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 110.0 KiB/110.0 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/outputs/reports.h5\nCompleted 92.9 KiB/117.0 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/output.zip\nCompleted 92.9 KiB/117.0 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 101.6 KiB/117.0 KiB (979.8 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/outputs/plots.zip\nCompleted 101.6 KiB/117.0 KiB (979.8 KiB/s) with 2 file(s) remaining\rCompleted 114.3 KiB/117.0 KiB (1.0 MiB/s) with 2 file(s) remaining  \rupload: outputs/BIOMD0000000330_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/outputs/BIOMD0000000330_url.sedml/autogen_plot_for_task1.pdf\nCompleted 114.3 KiB/117.0 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 117.0 KiB/117.0 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000330-biopax2.owl  \n  inflating: contents/BIOMD0000000330-biopax3.owl  \n  inflating: contents/BIOMD0000000330-matlab.m  \n  inflating: contents/BIOMD0000000330-octave.m  \n  inflating: contents/BIOMD0000000330.m  \n  inflating: contents/BIOMD0000000330.ode  \n  inflating: contents/BIOMD0000000330.pdf  \n  inflating: contents/BIOMD0000000330.png  \n  inflating: contents/BIOMD0000000330.sci  \n  inflating: contents/BIOMD0000000330.svg  \n  inflating: contents/BIOMD0000000330_url.sedml  \n  inflating: contents/BIOMD0000000330_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 7.8 KiB/263.7 KiB (112.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000330-biopax3.owl to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330-biopax3.owl\nCompleted 7.8 KiB/263.7 KiB (112.2 KiB/s) with 15 file(s) remaining\rCompleted 12.9 KiB/263.7 KiB (132.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000330-matlab.m to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330-matlab.m\nCompleted 12.9 KiB/263.7 KiB (132.0 KiB/s) with 14 file(s) remaining\rCompleted 15.5 KiB/263.7 KiB (120.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000330.sci to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330.sci\nCompleted 15.5 KiB/263.7 KiB (120.2 KiB/s) with 13 file(s) remaining\rCompleted 20.6 KiB/263.7 KiB (157.6 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000330-octave.m to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330-octave.m\nCompleted 20.6 KiB/263.7 KiB (157.6 KiB/s) with 12 file(s) remaining\rCompleted 20.8 KiB/263.7 KiB (157.1 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/curation_notes.txt\nCompleted 20.8 KiB/263.7 KiB (157.1 KiB/s) with 11 file(s) remaining\rCompleted 21.7 KiB/263.7 KiB (145.1 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000330.svg to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330.svg\nCompleted 21.7 KiB/263.7 KiB (145.1 KiB/s) with 10 file(s) remaining\rCompleted 24.9 KiB/263.7 KiB (165.3 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/metadata.rdf\nCompleted 24.9 KiB/263.7 KiB (165.3 KiB/s) with 9 file(s) remaining\rCompleted 32.1 KiB/263.7 KiB (204.6 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000330-biopax2.owl to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330-biopax2.owl\nCompleted 32.1 KiB/263.7 KiB (204.6 KiB/s) with 8 file(s) remaining\rCompleted 48.4 KiB/263.7 KiB (299.4 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000330_url.sedml to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330_url.sedml\nCompleted 48.4 KiB/263.7 KiB (299.4 KiB/s) with 7 file(s) remaining\rCompleted 68.0 KiB/263.7 KiB (410.2 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000330_url.xml to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330_url.xml\nCompleted 68.0 KiB/263.7 KiB (410.2 KiB/s) with 6 file(s) remaining\rCompleted 73.1 KiB/263.7 KiB (389.0 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000330.png to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330.png\nCompleted 73.1 KiB/263.7 KiB (389.0 KiB/s) with 5 file(s) remaining\rCompleted 78.2 KiB/263.7 KiB (409.5 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000330.m to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330.m\nCompleted 78.2 KiB/263.7 KiB (409.5 KiB/s) with 4 file(s) remaining\rCompleted 118.5 KiB/263.7 KiB (594.4 KiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/curation_image.png\nCompleted 118.5 KiB/263.7 KiB (594.4 KiB/s) with 3 file(s) remaining\rCompleted 120.4 KiB/263.7 KiB (594.7 KiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/manifest.xml\nCompleted 120.4 KiB/263.7 KiB (594.7 KiB/s) with 2 file(s) remaining\rCompleted 123.4 KiB/263.7 KiB (600.0 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000330.ode to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330.ode\nCompleted 123.4 KiB/263.7 KiB (600.0 KiB/s) with 1 file(s) remaining\rCompleted 263.7 KiB/263.7 KiB (1.2 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000330.pdf to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/contents/BIOMD0000000330.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (125.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b4249c0d898ffde0e1f/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000330_url.sedml\ncreating dataset /BIOMD0000000330_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-97e90877-1a5f2e8d-9efb-ddbae2-f5ca9c, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000330_url.sedml/autogen_report_for_task1, shape: (30, 1001), type: float64\ndataset created, uuid: d-97e90877-1a5f2e8d-d379-7f4f3f-87a40c, chunk_size: (30, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000330_url.sedml\ncreating attribute uri in /BIOMD0000000330_url.sedml\ncreating attribute _type in /BIOMD0000000330_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000330_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000330_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000330_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000330_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000330_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000330_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000330_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000330_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000330_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000330_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000330_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000330_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000330_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000330_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000330_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000330_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000330_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000330_url.sedml\ncreate_links: /BIOMD0000000330_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000330_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000330_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000330_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000330_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000330_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000330_url.sedml/autogen_report_for_task1, shape: (30, 1001), type: float64\niterating over chunks for /BIOMD0000000330_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 30, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000330_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710b4249c0d898ffde0e1f\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.\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 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":15.953998,"sedDocuments":[{"location":"BIOMD0000000330_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  BIOMD0000000330_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 30 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000330_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":15.643074,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":14.888257,"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":0.23951,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_G_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_PLC","status":"SUCCEEDED"},{"id":"autogen_task1_Ca_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_Ca_ER","status":"SUCCEEDED"},{"id":"autogen_task1_Ca_mit","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_K4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_K6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k8","status":"SUCCEEDED"},{"id":"autogen_task1_K9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_K11","status":"SUCCEEDED"},{"id":"autogen_task1_k12","status":"SUCCEEDED"},{"id":"autogen_task1_k13","status":"SUCCEEDED"},{"id":"autogen_task1_k14","status":"SUCCEEDED"},{"id":"autogen_task1_K15","status":"SUCCEEDED"},{"id":"autogen_task1_k16","status":"SUCCEEDED"},{"id":"autogen_task1_K17","status":"SUCCEEDED"},{"id":"autogen_task1_k18","status":"SUCCEEDED"},{"id":"autogen_task1_K19","status":"SUCCEEDED"},{"id":"autogen_task1_k20","status":"SUCCEEDED"},{"id":"autogen_task1_K21","status":"SUCCEEDED"},{"id":"autogen_task1_cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_ER","status":"SUCCEEDED"},{"id":"autogen_task1_mit","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.378907,"curves":[{"id":"autogen_curve_task1_G_alpha","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PLC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca_ER","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca_mit","status":"SUCCEEDED"}]}]}]}