{"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    449      0 --:--:-- --:--:-- --:--:--   451\n\r100 59749  100 59749    0     0   142k      0 --:--:-- --:--:-- --:--:--  142k\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 (23.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/rawLog.txt\nCompleted 5.0 KiB/5.0 KiB (73.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/Cooper2015.sedml/ (stored 0%)\n  adding: outputs/Cooper2015.sedml/plot_1_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 13%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 210.3 KiB/210.3 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/outputs/reports.h5\nCompleted 193.9 KiB/217.2 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/output.zip\nCompleted 193.9 KiB/217.2 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 196.5 KiB/217.2 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/rawLog.txt\nCompleted 196.5 KiB/217.2 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 204.9 KiB/217.2 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/outputs/plots.zip\nCompleted 204.9 KiB/217.2 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 217.2 KiB/217.2 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/Cooper2015.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/outputs/Cooper2015.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Cooper2015-biopax2.owl  \n  inflating: contents/Cooper2015-biopax3.owl  \n  inflating: contents/Cooper2015-matlab.m  \n  inflating: contents/Cooper2015-octave.m  \n  inflating: contents/Cooper2015.cps  \n  inflating: contents/Cooper2015.ode  \n  inflating: contents/Cooper2015.sedml  \n  inflating: contents/Cooper2015.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 23.4 KiB/332.1 KiB (305.3 KiB/s) with 12 file(s) remaining\rupload: contents/Cooper2015-biopax3.owl to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/Cooper2015-biopax3.owl\nCompleted 23.4 KiB/332.1 KiB (305.3 KiB/s) with 11 file(s) remaining\rCompleted 40.2 KiB/332.1 KiB (331.7 KiB/s) with 11 file(s) remaining\rupload: contents/Cooper2015-biopax2.owl to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/Cooper2015-biopax2.owl\nCompleted 40.2 KiB/332.1 KiB (331.7 KiB/s) with 10 file(s) remaining\rCompleted 49.6 KiB/332.1 KiB (397.7 KiB/s) with 10 file(s) remaining\rupload: contents/Cooper2015-matlab.m to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/Cooper2015-matlab.m\nCompleted 49.6 KiB/332.1 KiB (397.7 KiB/s) with 9 file(s) remaining\rCompleted 49.8 KiB/332.1 KiB (370.1 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/curation_notes.txt\nCompleted 49.8 KiB/332.1 KiB (370.1 KiB/s) with 8 file(s) remaining\rCompleted 80.8 KiB/332.1 KiB (575.5 KiB/s) with 8 file(s) remaining\rupload: contents/Cooper2015.sedml to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/Cooper2015.sedml\nCompleted 80.8 KiB/332.1 KiB (575.5 KiB/s) with 7 file(s) remaining\rCompleted 90.2 KiB/332.1 KiB (617.5 KiB/s) with 7 file(s) remaining\rupload: contents/Cooper2015-octave.m to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/Cooper2015-octave.m\nCompleted 90.2 KiB/332.1 KiB (617.5 KiB/s) with 6 file(s) remaining\rCompleted 91.5 KiB/332.1 KiB (536.4 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/manifest.xml\nCompleted 91.5 KiB/332.1 KiB (536.4 KiB/s) with 5 file(s) remaining\rCompleted 125.0 KiB/332.1 KiB (686.4 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/curation_image.png\nCompleted 125.0 KiB/332.1 KiB (686.4 KiB/s) with 4 file(s) remaining\rCompleted 203.9 KiB/332.1 KiB (1.1 MiB/s) with 4 file(s) remaining  \rupload: contents/Cooper2015.xml to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/Cooper2015.xml\nCompleted 203.9 KiB/332.1 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 321.5 KiB/332.1 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/Cooper2015.cps to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/Cooper2015.cps\nCompleted 321.5 KiB/332.1 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 325.1 KiB/332.1 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/metadata.rdf\nCompleted 325.1 KiB/332.1 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 332.1 KiB/332.1 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/Cooper2015.ode to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/contents/Cooper2015.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.4 KiB/7.4 KiB (101.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711dfc49c0d898ffdf697b/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Cooper2015.sedml\ncreating dataset /Cooper2015.sedml/autogen_report_for_task1, shape: (57, 1001), type: float64\ndataset created, uuid: d-bc1aef3c-b9777d56-9d0e-a0f02d-3434bc, chunk_size: (57, 1001)\ncreating dataset /Cooper2015.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-bc1aef3c-b9777d56-e15a-3657f7-15d3cf, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /Cooper2015.sedml\ncreating attribute uri in /Cooper2015.sedml\ncreating attribute _type in /Cooper2015.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Cooper2015.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Cooper2015.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Cooper2015.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Cooper2015.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Cooper2015.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Cooper2015.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Cooper2015.sedml/autogen_report_for_task1\ncreating attribute uri in /Cooper2015.sedml/autogen_report_for_task1\ncreating attribute _type in /Cooper2015.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Cooper2015.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Cooper2015.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Cooper2015.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Cooper2015.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Cooper2015.sedml/plot_1_task1\ncreating attribute sedmlId in /Cooper2015.sedml/plot_1_task1\ncreating attribute sedmlName in /Cooper2015.sedml/plot_1_task1\ncreating attribute uri in /Cooper2015.sedml/plot_1_task1\ncreate_links: /\ngot link: Cooper2015.sedml\ncreate_links: /Cooper2015.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Cooper2015.sedml/autogen_report_for_task1 to tgt: /Cooper2015.sedml/autogen_report_for_task1, shape: (57, 1001), type: float64\niterating over chunks for /Cooper2015.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 57, 1), slice(0, 1001, 1))\ndone with dataload for /Cooper2015.sedml/autogen_report_for_task1\nwrite_dataset src: /Cooper2015.sedml/plot_1_task1 to tgt: /Cooper2015.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /Cooper2015.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Cooper2015.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711dfc49c0d898ffdf697b\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 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.\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 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":1.814033,"sedDocuments":[{"location":"Cooper2015.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  Cooper2015.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 57 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Cooper2015.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":1.328864,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.197437,"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":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.41928,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.527055,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Pt","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_kpn","status":"SUCCEEDED"},{"id":"autogen_task1_kpm","status":"SUCCEEDED"},{"id":"autogen_task1_Ninf","status":"SUCCEEDED"},{"id":"autogen_task1_kptn","status":"SUCCEEDED"},{"id":"autogen_task1_kptm","status":"SUCCEEDED"},{"id":"autogen_task1_mupt","status":"SUCCEEDED"},{"id":"autogen_task1_knp","status":"SUCCEEDED"},{"id":"autogen_task1_knpt","status":"SUCCEEDED"},{"id":"autogen_task1_snr","status":"SUCCEEDED"},{"id":"autogen_task1_munr","status":"SUCCEEDED"},{"id":"autogen_task1_mun","status":"SUCCEEDED"},{"id":"autogen_task1_knm","status":"SUCCEEDED"},{"id":"autogen_task1_kmp","status":"SUCCEEDED"},{"id":"autogen_task1_kmm","status":"SUCCEEDED"},{"id":"autogen_task1_kmn","status":"SUCCEEDED"},{"id":"autogen_task1_kmpt","status":"SUCCEEDED"},{"id":"autogen_task1_smr","status":"SUCCEEDED"},{"id":"autogen_task1_mumr","status":"SUCCEEDED"},{"id":"autogen_task1_mum","status":"SUCCEEDED"},{"id":"autogen_task1_fi2","status":"SUCCEEDED"},{"id":"autogen_task1_fEN","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_ENinf","status":"SUCCEEDED"},{"id":"autogen_task1_ken","status":"SUCCEEDED"},{"id":"autogen_task1_EMinf","status":"SUCCEEDED"},{"id":"autogen_task1_kem","status":"SUCCEEDED"},{"id":"autogen_task1_Cn","status":"SUCCEEDED"},{"id":"autogen_task1_Cm1","status":"SUCCEEDED"},{"id":"autogen_task1_Cm2","status":"SUCCEEDED"},{"id":"autogen_task1_kpg","status":"SUCCEEDED"},{"id":"autogen_task1_pinf","status":"SUCCEEDED"},{"id":"autogen_task1_kbp","status":"SUCCEEDED"},{"id":"autogen_task1_sb","status":"SUCCEEDED"},{"id":"autogen_task1_mub","status":"SUCCEEDED"},{"id":"autogen_task1_kpb","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_fEM_Kmm_E","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Pathogen_Growth","status":"SUCCEEDED"},{"id":"autogen_task1_Pathogen_Destruction_Background_Response","status":"SUCCEEDED"},{"id":"autogen_task1_Pathogen_Destruction_Neutrophils","status":"SUCCEEDED"},{"id":"autogen_task1_Pathogen_Destruction_Macrophages","status":"SUCCEEDED"},{"id":"autogen_task1_Debris_Destruction_Neutrophils","status":"SUCCEEDED"},{"id":"autogen_task1_Debris_Destruction_Macrophages","status":"SUCCEEDED"},{"id":"autogen_task1_Debris_Neutrophil_Decay","status":"SUCCEEDED"},{"id":"autogen_task1_Debris_Decay_Intrinsic","status":"SUCCEEDED"},{"id":"autogen_task1_Macrophage_Recruitment","status":"SUCCEEDED"},{"id":"autogen_task1_Macrophage_Activation","status":"SUCCEEDED"},{"id":"autogen_task1_Neutrophil_Activation","status":"SUCCEEDED"},{"id":"autogen_task1_Neutrophil_Destruction_Macrophage","status":"SUCCEEDED"}]}]}]}