{"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    431      0 --:--:-- --:--:-- --:--:--   431\n\r100  154k  100  154k    0     0   338k      0 --:--:-- --:--:-- --:--:--  338k\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/6471078b0dcacb55678b43ae/rawLog.txt\nCompleted 2.8 KiB/2.8 KiB (37.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/BIOMD0000000047_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000047_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 24%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 94.1 KiB/94.1 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/outputs/reports.h5\nCompleted 80.8 KiB/100.4 KiB (926.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/output.zip\nCompleted 80.8 KiB/100.4 KiB (926.6 KiB/s) with 3 file(s) remaining\rCompleted 90.9 KiB/100.4 KiB (820.3 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000047_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/outputs/BIOMD0000000047_url.sedml/autogen_plot_for_task1.pdf\nCompleted 90.9 KiB/100.4 KiB (820.3 KiB/s) with 2 file(s) remaining\rCompleted 97.7 KiB/100.4 KiB (864.2 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/outputs/plots.zip\nCompleted 97.7 KiB/100.4 KiB (864.2 KiB/s) with 1 file(s) remaining\rCompleted 100.4 KiB/100.4 KiB (863.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000047-biopax2.owl  \n  inflating: contents/BIOMD0000000047-biopax3.owl  \n  inflating: contents/BIOMD0000000047-matlab.m  \n  inflating: contents/BIOMD0000000047-octave.m  \n  inflating: contents/BIOMD0000000047.m  \n  inflating: contents/BIOMD0000000047.ode  \n  inflating: contents/BIOMD0000000047.pdf  \n  inflating: contents/BIOMD0000000047.png  \n  inflating: contents/BIOMD0000000047.svg  \n  inflating: contents/BIOMD0000000047_url.sedml  \n  inflating: contents/BIOMD0000000047_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 12.2 KiB/251.9 KiB (164.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000047-biopax3.owl to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047-biopax3.owl\nCompleted 12.2 KiB/251.9 KiB (164.3 KiB/s) with 14 file(s) remaining\rCompleted 21.8 KiB/251.9 KiB (192.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000047-biopax2.owl to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047-biopax2.owl\nCompleted 21.8 KiB/251.9 KiB (192.9 KiB/s) with 13 file(s) remaining\rCompleted 26.1 KiB/251.9 KiB (228.0 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000047-matlab.m to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047-matlab.m\nCompleted 26.1 KiB/251.9 KiB (228.0 KiB/s) with 12 file(s) remaining\rCompleted 26.2 KiB/251.9 KiB (184.0 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/curation_notes.txt\nCompleted 26.2 KiB/251.9 KiB (184.0 KiB/s) with 11 file(s) remaining\rCompleted 31.8 KiB/251.9 KiB (216.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000047.svg to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047.svg\nCompleted 31.8 KiB/251.9 KiB (216.7 KiB/s) with 10 file(s) remaining\rCompleted 43.4 KiB/251.9 KiB (286.2 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000047_url.sedml to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047_url.sedml\nCompleted 43.4 KiB/251.9 KiB (286.2 KiB/s) with 9 file(s) remaining\rCompleted 57.7 KiB/251.9 KiB (355.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000047_url.xml to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047_url.xml\nCompleted 57.7 KiB/251.9 KiB (355.0 KiB/s) with 8 file(s) remaining\rCompleted 75.0 KiB/251.9 KiB (423.0 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/curation_image.jpeg\nCompleted 75.0 KiB/251.9 KiB (423.0 KiB/s) with 7 file(s) remaining\rCompleted 79.4 KiB/251.9 KiB (436.3 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000047-octave.m to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047-octave.m\nCompleted 79.4 KiB/251.9 KiB (436.3 KiB/s) with 6 file(s) remaining\rCompleted 91.2 KiB/251.9 KiB (494.0 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000047.png to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047.png\nCompleted 91.2 KiB/251.9 KiB (494.0 KiB/s) with 5 file(s) remaining\rCompleted 92.9 KiB/251.9 KiB (497.4 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/manifest.xml\nCompleted 92.9 KiB/251.9 KiB (497.4 KiB/s) with 4 file(s) remaining\rCompleted 96.4 KiB/251.9 KiB (509.3 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/metadata.rdf\nCompleted 96.4 KiB/251.9 KiB (509.3 KiB/s) with 3 file(s) remaining\rCompleted 245.2 KiB/251.9 KiB (1.2 MiB/s) with 3 file(s) remaining \rupload: contents/BIOMD0000000047.pdf to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047.pdf\nCompleted 245.2 KiB/251.9 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 249.5 KiB/251.9 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000047.m to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047.m\nCompleted 249.5 KiB/251.9 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 251.9 KiB/251.9 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000047.ode to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/contents/BIOMD0000000047.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (124.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471078b0dcacb55678b43ae/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000047_url.sedml\ncreating dataset /BIOMD0000000047_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-639b312a-fb8c9ef6-129c-68070e-e0ce82, chunk_size: (3, 1001)\ncreating dataset /BIOMD0000000047_url.sedml/autogen_report_for_task1, shape: (21, 1001), type: float64\ndataset created, uuid: d-639b312a-fb8c9ef6-4399-77bf04-278a40, chunk_size: (21, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000047_url.sedml\ncreating attribute uri in /BIOMD0000000047_url.sedml\ncreating attribute _type in /BIOMD0000000047_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000047_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000047_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000047_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000047_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000047_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000047_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000047_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000047_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000047_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000047_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000047_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000047_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000047_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000047_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000047_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000047_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000047_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000047_url.sedml\ncreate_links: /BIOMD0000000047_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000047_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000047_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\niterating over chunks for /BIOMD0000000047_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000047_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000047_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000047_url.sedml/autogen_report_for_task1, shape: (21, 1001), type: float64\niterating over chunks for /BIOMD0000000047_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 21, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000047_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471078b0dcacb55678b43ae\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess 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 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":20.56061,"sedDocuments":[{"location":"BIOMD0000000047_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  BIOMD0000000047_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 21 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000047_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":20.22785,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":19.650525,"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":0.212653,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_CaER","status":"SUCCEEDED"},{"id":"autogen_task1_Ca_Cyt","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_n0","status":"SUCCEEDED"},{"id":"autogen_task1_kbN","status":"SUCCEEDED"},{"id":"autogen_task1_kappa","status":"SUCCEEDED"},{"id":"autogen_task1_p1","status":"SUCCEEDED"},{"id":"autogen_task1_p11","status":"SUCCEEDED"},{"id":"autogen_task1_p12","status":"SUCCEEDED"},{"id":"autogen_task1_K1","status":"SUCCEEDED"},{"id":"autogen_task1_p2","status":"SUCCEEDED"},{"id":"autogen_task1_K2","status":"SUCCEEDED"},{"id":"autogen_task1_p3","status":"SUCCEEDED"},{"id":"autogen_task1_k31","status":"SUCCEEDED"},{"id":"autogen_task1_K3","status":"SUCCEEDED"},{"id":"autogen_task1_Cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_Endoplasmic_Reticulum","status":"SUCCEEDED"},{"id":"autogen_task1_Jch","status":"SUCCEEDED"},{"id":"autogen_task1_Jleak","status":"SUCCEEDED"},{"id":"autogen_task1_Jpump","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.230985,"curves":[{"id":"autogen_curve_task1_CaER","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ca_Cyt","status":"SUCCEEDED"}]}]}]}