{"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    423      0 --:--:-- --:--:-- --:--:--   422\n\r100  373k  100  373k    0     0   818k      0 --:--:-- --:--:-- --:--:--  818k\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 (25.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/rawLog.txt\nCompleted 5.8 KiB/5.8 KiB (88.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/MODEL1006230097.sedml/ (stored 0%)\n  adding: outputs/MODEL1006230097.sedml/plot_1_task1.pdf (deflated 35%)\n  adding: outputs/reports.h5 (deflated 22%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 133.0 KiB/133.0 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/outputs/reports.h5\nCompleted 111.2 KiB/126.7 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/output.zip\nCompleted 111.2 KiB/126.7 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 116.2 KiB/126.7 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/outputs/plots.zip\nCompleted 116.2 KiB/126.7 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 124.0 KiB/126.7 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: outputs/MODEL1006230097.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/outputs/MODEL1006230097.sedml/plot_1_task1.pdf\nCompleted 124.0 KiB/126.7 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 126.7 KiB/126.7 KiB (588.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000688-biopax2.owl  \n  inflating: contents/BIOMD0000000688-biopax3.owl  \n  inflating: contents/BIOMD0000000688-matlab.m  \n  inflating: contents/BIOMD0000000688.m  \n  inflating: contents/BIOMD0000000688.ode  \n  inflating: contents/BIOMD0000000688.pdf  \n  inflating: contents/BIOMD0000000688.png  \n  inflating: contents/BIOMD0000000688.svg  \n  inflating: contents/BIOMD0000000688_url.xml  \n  inflating: contents/MODEL1006230097.cps  \n  inflating: contents/MODEL1006230097.sedml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 57.8 KiB/820.1 KiB (551.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000688-biopax3.owl to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/BIOMD0000000688-biopax3.owl\nCompleted 57.8 KiB/820.1 KiB (551.1 KiB/s) with 14 file(s) remaining\rCompleted 69.9 KiB/820.1 KiB (644.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000688-matlab.m to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/BIOMD0000000688-matlab.m\nCompleted 69.9 KiB/820.1 KiB (644.5 KiB/s) with 13 file(s) remaining\rCompleted 82.0 KiB/820.1 KiB (609.4 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000688.m to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/BIOMD0000000688.m\nCompleted 82.0 KiB/820.1 KiB (609.4 KiB/s) with 12 file(s) remaining\rCompleted 118.2 KiB/820.1 KiB (837.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000688-biopax2.owl to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/BIOMD0000000688-biopax2.owl\nCompleted 118.2 KiB/820.1 KiB (837.7 KiB/s) with 11 file(s) remaining\rCompleted 156.3 KiB/820.1 KiB (993.3 KiB/s) with 11 file(s) remaining\rupload: contents/MODEL1006230097.sedml to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/MODEL1006230097.sedml\nCompleted 156.3 KiB/820.1 KiB (993.3 KiB/s) with 10 file(s) remaining\rCompleted 266.0 KiB/820.1 KiB (1.6 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000688_url.xml to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/BIOMD0000000688_url.xml\nCompleted 266.0 KiB/820.1 KiB (1.6 MiB/s) with 9 file(s) remaining\rCompleted 279.5 KiB/820.1 KiB (1.7 MiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/curation_image.png\nCompleted 279.5 KiB/820.1 KiB (1.7 MiB/s) with 8 file(s) remaining\rCompleted 279.7 KiB/820.1 KiB (1.6 MiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/curation_notes.txt\nCompleted 279.7 KiB/820.1 KiB (1.6 MiB/s) with 7 file(s) remaining\rCompleted 285.4 KiB/820.1 KiB (1.6 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/metadata.rdf\nCompleted 285.4 KiB/820.1 KiB (1.6 MiB/s) with 6 file(s) remaining\rCompleted 412.5 KiB/820.1 KiB (2.2 MiB/s) with 6 file(s) remaining\rupload: contents/MODEL1006230097.cps to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/MODEL1006230097.cps\nCompleted 412.5 KiB/820.1 KiB (2.2 MiB/s) with 5 file(s) remaining\rCompleted 532.2 KiB/820.1 KiB (2.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000688.png to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/BIOMD0000000688.png\nCompleted 532.2 KiB/820.1 KiB (2.8 MiB/s) with 4 file(s) remaining\rCompleted 533.9 KiB/820.1 KiB (2.8 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/manifest.xml\nCompleted 533.9 KiB/820.1 KiB (2.8 MiB/s) with 3 file(s) remaining\rCompleted 542.1 KiB/820.1 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000688.ode to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/BIOMD0000000688.ode\nCompleted 542.1 KiB/820.1 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 606.2 KiB/820.1 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000688.svg to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/BIOMD0000000688.svg\nCompleted 606.2 KiB/820.1 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 820.1 KiB/820.1 KiB (3.0 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000688.pdf to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/contents/BIOMD0000000688.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (115.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c3a49c0d898ffdf24bc/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /MODEL1006230097.sedml\ncreating dataset /MODEL1006230097.sedml/autogen_report_for_task1, shape: (68, 501), type: float64\ndataset created, uuid: d-2c5671d7-0ee7c338-450e-185aae-0641ea, chunk_size: (68, 501)\ncreating dataset /MODEL1006230097.sedml/plot_1_task1, shape: (2, 501), type: float64\ndataset created, uuid: d-2c5671d7-0ee7c338-bef2-dc71ad-41ca86, chunk_size: (2, 501)\ncreating attribute combineArchiveLocation in /MODEL1006230097.sedml\ncreating attribute uri in /MODEL1006230097.sedml\ncreating attribute _type in /MODEL1006230097.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1006230097.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /MODEL1006230097.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /MODEL1006230097.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /MODEL1006230097.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /MODEL1006230097.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /MODEL1006230097.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /MODEL1006230097.sedml/autogen_report_for_task1\ncreating attribute uri in /MODEL1006230097.sedml/autogen_report_for_task1\ncreating attribute _type in /MODEL1006230097.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1006230097.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /MODEL1006230097.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /MODEL1006230097.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /MODEL1006230097.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /MODEL1006230097.sedml/plot_1_task1\ncreating attribute sedmlId in /MODEL1006230097.sedml/plot_1_task1\ncreating attribute sedmlName in /MODEL1006230097.sedml/plot_1_task1\ncreating attribute uri in /MODEL1006230097.sedml/plot_1_task1\ncreate_links: /\ngot link: MODEL1006230097.sedml\ncreate_links: /MODEL1006230097.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /MODEL1006230097.sedml/autogen_report_for_task1 to tgt: /MODEL1006230097.sedml/autogen_report_for_task1, shape: (68, 501), type: float64\niterating over chunks for /MODEL1006230097.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 68, 1), slice(0, 501, 1))\ndone with dataload for /MODEL1006230097.sedml/autogen_report_for_task1\nwrite_dataset src: /MODEL1006230097.sedml/plot_1_task1 to tgt: /MODEL1006230097.sedml/plot_1_task1, shape: (2, 501), type: float64\niterating over chunks for /MODEL1006230097.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 501, 1))\ndone with dataload for /MODEL1006230097.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c3a49c0d898ffdf24bc\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 and upload the outputs of the simulation run ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.501388,"sedDocuments":[{"location":"MODEL1006230097.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  MODEL1006230097.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 68 data sets\r\n    Plots (1):\r\n      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: MODEL1006230097.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":1.014209,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.217939,"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":0.321255,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.292083,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_z_i","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_y_0","status":"SUCCEEDED"},{"id":"autogen_task1_y_1","status":"SUCCEEDED"},{"id":"autogen_task1_L","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_z_a","status":"SUCCEEDED"},{"id":"autogen_task1_m_0","status":"SUCCEEDED"},{"id":"autogen_task1_m_1","status":"SUCCEEDED"},{"id":"autogen_task1_m_2","status":"SUCCEEDED"},{"id":"autogen_task1_m_3","status":"SUCCEEDED"},{"id":"autogen_task1_m_4","status":"SUCCEEDED"},{"id":"autogen_task1_m_5","status":"SUCCEEDED"},{"id":"autogen_task1_m_6","status":"SUCCEEDED"},{"id":"autogen_task1_m_7","status":"SUCCEEDED"},{"id":"autogen_task1_m_8","status":"SUCCEEDED"},{"id":"autogen_task1_R0","status":"SUCCEEDED"},{"id":"autogen_task1_a0","status":"SUCCEEDED"},{"id":"autogen_task1_a1","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_lambda","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_phi","status":"SUCCEEDED"},{"id":"autogen_task1_eta","status":"SUCCEEDED"},{"id":"autogen_task1_pa","status":"SUCCEEDED"},{"id":"autogen_task1_ca","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_ba","status":"SUCCEEDED"},{"id":"autogen_task1_p_i","status":"SUCCEEDED"},{"id":"autogen_task1_ci","status":"SUCCEEDED"},{"id":"autogen_task1_bi","status":"SUCCEEDED"},{"id":"autogen_task1_xi","status":"SUCCEEDED"},{"id":"autogen_task1_COMpartment","status":"SUCCEEDED"},{"id":"autogen_task1_Host_cell_proliferation","status":"SUCCEEDED"},{"id":"autogen_task1_Host_cell_death","status":"SUCCEEDED"},{"id":"autogen_task1_Infection_1","status":"SUCCEEDED"},{"id":"autogen_task1_Infection_2","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_cell_death_1","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_cell_infection_progression_1","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_cell_infection_progression_2","status":"SUCCEEDED"},{"id":"autogen_task1_CTL_induced_infected_cell_death_1","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_cell_death_2","status":"SUCCEEDED"},{"id":"autogen_task1_CTL_induced_infected_cell_death_2","status":"SUCCEEDED"},{"id":"autogen_task1_Infected_cell_death_3","status":"SUCCEEDED"},{"id":"autogen_task1_Virus_particle_production","status":"SUCCEEDED"},{"id":"autogen_task1_Viral_particle_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_Precursor_T_cell_differentiation_2","status":"SUCCEEDED"},{"id":"autogen_task1_Infection_induced_CTL_proliferation_stimulation","status":"SUCCEEDED"},{"id":"autogen_task1_CTL_cell_death","status":"SUCCEEDED"},{"id":"autogen_task1_Naive_CTL_division_1","status":"SUCCEEDED"},{"id":"autogen_task1_Naive_CTL_division_2","status":"SUCCEEDED"},{"id":"autogen_task1_Naive_CTL_division_3","status":"SUCCEEDED"},{"id":"autogen_task1_Naive_CTL_division_4","status":"SUCCEEDED"},{"id":"autogen_task1_Naive_CTL_division_5","status":"SUCCEEDED"},{"id":"autogen_task1_Naive_CTL_division_6","status":"SUCCEEDED"},{"id":"autogen_task1_Naive_CTL_division_7","status":"SUCCEEDED"},{"id":"autogen_task1_Naive_CTL_division_8","status":"SUCCEEDED"},{"id":"autogen_task1_Precursor_T_cell_differentiation_1","status":"SUCCEEDED"},{"id":"autogen_task1_NK_cell_production","status":"SUCCEEDED"},{"id":"autogen_task1_NK_infection_induced_production","status":"SUCCEEDED"},{"id":"autogen_task1_NK_cell_death","status":"SUCCEEDED"},{"id":"autogen_task1_NK_induced_infected_cell_death_1","status":"SUCCEEDED"},{"id":"autogen_task1_NK_induced_infected_cell_death_2","status":"SUCCEEDED"}]}]}]}