{"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    421      0 --:--:-- --:--:-- --:--:--   422\n\r100  237k  100  237k    0     0   518k      0 --:--:-- --:--:-- --:--:--  518k\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 (22.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/rawLog.txt\nCompleted 3.8 KiB/3.8 KiB (61.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/BIOMD0000000251_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000251_url.sedml/autogen_plot_for_task1.pdf (deflated 27%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 245.5 KiB/245.5 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/outputs/reports.h5\nCompleted 232.2 KiB/258.4 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/output.zip\nCompleted 232.2 KiB/258.4 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 242.0 KiB/258.4 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/outputs/plots.zip\nCompleted 242.0 KiB/258.4 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 255.8 KiB/258.4 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000251_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/outputs/BIOMD0000000251_url.sedml/autogen_plot_for_task1.pdf\nCompleted 255.8 KiB/258.4 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 258.4 KiB/258.4 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000251-biopax2.owl  \n  inflating: contents/BIOMD0000000251-biopax3.owl  \n  inflating: contents/BIOMD0000000251-matlab.m  \n  inflating: contents/BIOMD0000000251-octave.m  \n  inflating: contents/BIOMD0000000251.m  \n  inflating: contents/BIOMD0000000251.ode  \n  inflating: contents/BIOMD0000000251.pdf  \n  inflating: contents/BIOMD0000000251.png  \n  inflating: contents/BIOMD0000000251.svg  \n  inflating: contents/BIOMD0000000251.vcml  \n  inflating: contents/BIOMD0000000251_url.sedml  \n  inflating: contents/BIOMD0000000251_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 27.9 KiB/477.2 KiB (365.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000251-biopax3.owl to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251-biopax3.owl\nCompleted 27.9 KiB/477.2 KiB (365.2 KiB/s) with 15 file(s) remaining\rCompleted 34.4 KiB/477.2 KiB (301.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000251-matlab.m to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251-matlab.m\nCompleted 34.4 KiB/477.2 KiB (301.5 KiB/s) with 14 file(s) remaining\rCompleted 40.8 KiB/477.2 KiB (334.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000251-octave.m to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251-octave.m\nCompleted 40.8 KiB/477.2 KiB (334.7 KiB/s) with 13 file(s) remaining\rCompleted 41.0 KiB/477.2 KiB (311.7 KiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/curation_notes.txt\nCompleted 41.0 KiB/477.2 KiB (311.7 KiB/s) with 12 file(s) remaining\rCompleted 63.9 KiB/477.2 KiB (472.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000251-biopax2.owl to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251-biopax2.owl\nCompleted 63.9 KiB/477.2 KiB (472.9 KiB/s) with 11 file(s) remaining\rCompleted 86.2 KiB/477.2 KiB (582.6 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000251.svg to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251.svg\nCompleted 86.2 KiB/477.2 KiB (582.6 KiB/s) with 10 file(s) remaining\rCompleted 142.1 KiB/477.2 KiB (892.1 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000251.vcml to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251.vcml\nCompleted 142.1 KiB/477.2 KiB (892.1 KiB/s) with 9 file(s) remaining\rCompleted 159.1 KiB/477.2 KiB (981.1 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000251_url.sedml to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251_url.sedml\nCompleted 159.1 KiB/477.2 KiB (981.1 KiB/s) with 8 file(s) remaining\rCompleted 165.3 KiB/477.2 KiB (936.5 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/metadata.rdf\nCompleted 165.3 KiB/477.2 KiB (936.5 KiB/s) with 7 file(s) remaining\rCompleted 203.6 KiB/477.2 KiB (1.1 MiB/s) with 7 file(s) remaining  \rupload: contents/BIOMD0000000251_url.xml to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251_url.xml\nCompleted 203.6 KiB/477.2 KiB (1.1 MiB/s) with 6 file(s) remaining\rCompleted 205.5 KiB/477.2 KiB (1.0 MiB/s) with 6 file(s) remaining\rCompleted 212.1 KiB/477.2 KiB (1.1 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/curation_image.png\nCompleted 212.1 KiB/477.2 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/manifest.xml\nCompleted 212.1 KiB/477.2 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 283.3 KiB/477.2 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000251.png to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251.png\nCompleted 283.3 KiB/477.2 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 466.8 KiB/477.2 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000251.pdf to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251.pdf\nCompleted 466.8 KiB/477.2 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 470.7 KiB/477.2 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000251.ode to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251.ode\nCompleted 470.7 KiB/477.2 KiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 477.2 KiB/477.2 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000251.m to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/contents/BIOMD0000000251.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (132.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a3a9a62a8be53f7977e/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000251_url.sedml\ncreating dataset /BIOMD0000000251_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\ndataset created, uuid: d-2542b36d-e04c1ecf-d169-fa237b-b6528c, chunk_size: (11, 1001)\ncreating dataset /BIOMD0000000251_url.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\ndataset created, uuid: d-2542b36d-e04c1ecf-d67a-460c2d-51c7d5, chunk_size: (29, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000251_url.sedml\ncreating attribute uri in /BIOMD0000000251_url.sedml\ncreating attribute _type in /BIOMD0000000251_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000251_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000251_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000251_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000251_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000251_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000251_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000251_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000251_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000251_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000251_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000251_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000251_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000251_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000251_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000251_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000251_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000251_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000251_url.sedml\ncreate_links: /BIOMD0000000251_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000251_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000251_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\niterating over chunks for /BIOMD0000000251_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000251_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000251_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000251_url.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\niterating over chunks for /BIOMD0000000251_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 29, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000251_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710a3a9a62a8be53f7977e\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 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.\nProcess and upload the outputs of the simulation run ... 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":20.179986,"sedDocuments":[{"location":"BIOMD0000000251_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  BIOMD0000000251_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 29 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 10 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000251_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":19.827504,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":18.893618,"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":0.261323,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x1","status":"SUCCEEDED"},{"id":"autogen_task1_x2","status":"SUCCEEDED"},{"id":"autogen_task1_ppERKn","status":"SUCCEEDED"},{"id":"autogen_task1_DUSP","status":"SUCCEEDED"},{"id":"autogen_task1_pRSKn","status":"SUCCEEDED"},{"id":"autogen_task1_cFOSp","status":"SUCCEEDED"},{"id":"autogen_task1_cFOS","status":"SUCCEEDED"},{"id":"autogen_task1_pcFOS","status":"SUCCEEDED"},{"id":"autogen_task1_cFOSm","status":"SUCCEEDED"},{"id":"autogen_task1_ppERKc","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k11","status":"SUCCEEDED"},{"id":"autogen_task1_k13","status":"SUCCEEDED"},{"id":"autogen_task1_L","status":"SUCCEEDED"},{"id":"autogen_task1_K1","status":"SUCCEEDED"},{"id":"autogen_task1_tau1","status":"SUCCEEDED"},{"id":"autogen_task1_K2","status":"SUCCEEDED"},{"id":"autogen_task1_tau2","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_7","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_8","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_9","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.530062,"curves":[{"id":"autogen_curve_task1_x1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ppERKn","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DUSP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pRSKn","status":"SUCCEEDED"},{"id":"autogen_curve_task1_cFOSp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_cFOS","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pcFOS","status":"SUCCEEDED"},{"id":"autogen_curve_task1_cFOSm","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ppERKc","status":"SUCCEEDED"}]}]}]}