{"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 --:--:-- --:--:-- --:--:--   446\n\r100 52280  100 52280    0     0   119k      0 --:--:-- --:--:-- --:--:--  119k\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 (13.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/rawLog.txt\nCompleted 3.5 KiB/3.5 KiB (26.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/reports.h5 (deflated 28%)\n  adding: outputs/LeBeau1999_Phosphorylation_CCK.sedml/ (stored 0%)\n  adding: outputs/LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1.pdf (deflated 28%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 90.0 KiB/90.0 KiB (708.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/outputs/reports.h5\nCompleted 75.3 KiB/96.4 KiB (725.0 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/output.zip\nCompleted 75.3 KiB/96.4 KiB (725.0 KiB/s) with 3 file(s) remaining\rCompleted 82.9 KiB/96.4 KiB (726.5 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/outputs/plots.zip\nCompleted 82.9 KiB/96.4 KiB (726.5 KiB/s) with 2 file(s) remaining\rCompleted 93.7 KiB/96.4 KiB (785.7 KiB/s) with 2 file(s) remaining\rupload: outputs/LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/outputs/LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1.pdf\nCompleted 93.7 KiB/96.4 KiB (785.7 KiB/s) with 1 file(s) remaining\rCompleted 96.4 KiB/96.4 KiB (569.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/LeBeau1999_Phosphorylation_CCK-biopax2.owl  \n  inflating: contents/LeBeau1999_Phosphorylation_CCK-biopax3.owl  \n  inflating: contents/LeBeau1999_Phosphorylation_CCK-matlab.m  \n  inflating: contents/LeBeau1999_Phosphorylation_CCK-octave.m  \n  inflating: contents/LeBeau1999_Phosphorylation_CCK.cps  \n  inflating: contents/LeBeau1999_Phosphorylation_CCK.ode  \n  inflating: contents/LeBeau1999_Phosphorylation_CCK.sedml  \n  inflating: contents/LeBeau1999_Phosphorylation_CCK.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 21.1 KiB/335.0 KiB (266.5 KiB/s) with 12 file(s) remaining\rupload: contents/LeBeau1999_Phosphorylation_CCK-biopax3.owl to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/LeBeau1999_Phosphorylation_CCK-biopax3.owl\nCompleted 21.1 KiB/335.0 KiB (266.5 KiB/s) with 11 file(s) remaining\rCompleted 27.8 KiB/335.0 KiB (226.0 KiB/s) with 11 file(s) remaining\rupload: contents/LeBeau1999_Phosphorylation_CCK-matlab.m to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/LeBeau1999_Phosphorylation_CCK-matlab.m\nCompleted 27.8 KiB/335.0 KiB (226.0 KiB/s) with 10 file(s) remaining\rCompleted 45.4 KiB/335.0 KiB (292.5 KiB/s) with 10 file(s) remaining\rupload: contents/LeBeau1999_Phosphorylation_CCK.sedml to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/LeBeau1999_Phosphorylation_CCK.sedml\nCompleted 45.4 KiB/335.0 KiB (292.5 KiB/s) with 9 file(s) remaining\rCompleted 58.7 KiB/335.0 KiB (372.2 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/curation_image.png\nCompleted 58.7 KiB/335.0 KiB (372.2 KiB/s) with 8 file(s) remaining\rCompleted 58.9 KiB/335.0 KiB (367.1 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/curation_notes.txt\nCompleted 58.9 KiB/335.0 KiB (367.1 KiB/s) with 7 file(s) remaining\rCompleted 74.1 KiB/335.0 KiB (448.4 KiB/s) with 7 file(s) remaining\rupload: contents/LeBeau1999_Phosphorylation_CCK-biopax2.owl to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/LeBeau1999_Phosphorylation_CCK-biopax2.owl\nCompleted 74.1 KiB/335.0 KiB (448.4 KiB/s) with 6 file(s) remaining\rCompleted 80.8 KiB/335.0 KiB (421.0 KiB/s) with 6 file(s) remaining\rupload: contents/LeBeau1999_Phosphorylation_CCK-octave.m to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/LeBeau1999_Phosphorylation_CCK-octave.m\nCompleted 80.8 KiB/335.0 KiB (421.0 KiB/s) with 5 file(s) remaining\rCompleted 84.5 KiB/335.0 KiB (404.9 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/metadata.rdf\nCompleted 84.5 KiB/335.0 KiB (404.9 KiB/s) with 4 file(s) remaining\rCompleted 86.1 KiB/335.0 KiB (405.2 KiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/manifest.xml\nCompleted 86.1 KiB/335.0 KiB (405.2 KiB/s) with 3 file(s) remaining\rCompleted 206.7 KiB/335.0 KiB (934.0 KiB/s) with 3 file(s) remaining\rupload: contents/LeBeau1999_Phosphorylation_CCK.cps to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/LeBeau1999_Phosphorylation_CCK.cps\nCompleted 206.7 KiB/335.0 KiB (934.0 KiB/s) with 2 file(s) remaining\rCompleted 211.4 KiB/335.0 KiB (936.1 KiB/s) with 2 file(s) remaining\rupload: contents/LeBeau1999_Phosphorylation_CCK.ode to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/LeBeau1999_Phosphorylation_CCK.ode\nCompleted 211.4 KiB/335.0 KiB (936.1 KiB/s) with 1 file(s) remaining\rCompleted 335.0 KiB/335.0 KiB (1.4 MiB/s) with 1 file(s) remaining  \rupload: contents/LeBeau1999_Phosphorylation_CCK.xml to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/contents/LeBeau1999_Phosphorylation_CCK.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.9 KiB/7.9 KiB (71.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a5caf77b6669655063248/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /LeBeau1999_Phosphorylation_CCK.sedml\ncreating dataset /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1, shape: (32, 501), type: float64\ndataset created, uuid: d-5a7ca9a3-030979c3-07fd-e8d5f5-b06d74, chunk_size: (32, 501)\ncreating dataset /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1, shape: (2, 501), type: float64\ndataset created, uuid: d-5a7ca9a3-030979c3-23b3-87cfea-8658dd, chunk_size: (2, 501)\ncreating attribute combineArchiveLocation in /LeBeau1999_Phosphorylation_CCK.sedml\ncreating attribute uri in /LeBeau1999_Phosphorylation_CCK.sedml\ncreating attribute _type in /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\ncreating attribute uri in /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\ncreating attribute _type in /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\ncreating attribute sedmlId in /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\ncreating attribute sedmlName in /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\ncreating attribute uri in /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\ncreate_links: /\ngot link: LeBeau1999_Phosphorylation_CCK.sedml\ncreate_links: /LeBeau1999_Phosphorylation_CCK.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1 to tgt: /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1, shape: (32, 501), type: float64\niterating over chunks for /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 32, 1), slice(0, 501, 1))\ndone with dataload for /LeBeau1999_Phosphorylation_CCK.sedml/autogen_report_for_task1\nwrite_dataset src: /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1 to tgt: /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1, shape: (2, 501), type: float64\niterating over chunks for /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 501, 1))\ndone with dataload for /LeBeau1999_Phosphorylation_CCK.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a5caf77b6669655063248\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 and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.416415,"sedDocuments":[{"location":"LeBeau1999_Phosphorylation_CCK.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  LeBeau1999_Phosphorylation_CCK.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 32 data sets\r\n    Plots (1):\r\n      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: LeBeau1999_Phosphorylation_CCK.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":0.949216,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.253558,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":100000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.347218,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.172148,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_O","status":"SUCCEEDED"},{"id":"autogen_task1_I1","status":"SUCCEEDED"},{"id":"autogen_task1_I2","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_beta1","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_alpha4","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_beta4","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_time_constant","status":"SUCCEEDED"},{"id":"autogen_task1_kflux","status":"SUCCEEDED"},{"id":"autogen_task1_Vp","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k_1","status":"SUCCEEDED"},{"id":"autogen_task1_Jinflux_0","status":"SUCCEEDED"},{"id":"autogen_task1_Kp","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Shut_to_Open","status":"SUCCEEDED"},{"id":"autogen_task1_Open_to_Inactivated1","status":"SUCCEEDED"},{"id":"autogen_task1_Inactivated1_to_Shut","status":"SUCCEEDED"},{"id":"autogen_task1_Inactivated1_to_Inactivated2","status":"SUCCEEDED"},{"id":"autogen_task1_Inactivated2_to_Shut","status":"SUCCEEDED"},{"id":"autogen_task1_Jrel","status":"SUCCEEDED"},{"id":"autogen_task1_Jpump","status":"SUCCEEDED"},{"id":"autogen_task1_Jinflux","status":"SUCCEEDED"}]}]}]}