{"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    438      0 --:--:-- --:--:-- --:--:--   438\n\r100  333k  100  333k    0     0   759k      0 --:--:-- --:--:-- --:--:--  759k\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 (24.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/rawLog.txt\nCompleted 5.6 KiB/5.6 KiB (77.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/MODEL1006230052.sedml/ (stored 0%)\n  adding: outputs/MODEL1006230052.sedml/plot_1_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 248.8 KiB/248.8 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/outputs/reports.h5\nCompleted 227.5 KiB/245.2 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/output.zip\nCompleted 227.5 KiB/245.2 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 233.6 KiB/245.2 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/outputs/plots.zip\nCompleted 233.6 KiB/245.2 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 236.2 KiB/245.2 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/rawLog.txt\nCompleted 236.2 KiB/245.2 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 245.2 KiB/245.2 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/MODEL1006230052.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/outputs/MODEL1006230052.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000687-biopax2.owl  \n  inflating: contents/BIOMD0000000687-biopax3.owl  \n  inflating: contents/BIOMD0000000687-matlab.m  \n  inflating: contents/BIOMD0000000687.m  \n  inflating: contents/BIOMD0000000687.ode  \n  inflating: contents/BIOMD0000000687.pdf  \n  inflating: contents/BIOMD0000000687.png  \n  inflating: contents/BIOMD0000000687.svg  \n  inflating: contents/BIOMD0000000687.vcml  \n  inflating: contents/BIOMD0000000687_url.xml  \n  inflating: contents/MODEL1006230052.cps  \n  inflating: contents/MODEL1006230052.sedml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 50.8 KiB/843.4 KiB (538.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000687-biopax3.owl to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/BIOMD0000000687-biopax3.owl\nCompleted 50.8 KiB/843.4 KiB (538.5 KiB/s) with 15 file(s) remaining\rCompleted 61.6 KiB/843.4 KiB (591.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000687-matlab.m to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/BIOMD0000000687-matlab.m\nCompleted 61.6 KiB/843.4 KiB (591.7 KiB/s) with 14 file(s) remaining\rCompleted 72.3 KiB/843.4 KiB (607.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000687.m to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/BIOMD0000000687.m\nCompleted 72.3 KiB/843.4 KiB (607.5 KiB/s) with 13 file(s) remaining\rCompleted 104.2 KiB/843.4 KiB (840.4 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000687-biopax2.owl to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/BIOMD0000000687-biopax2.owl\nCompleted 104.2 KiB/843.4 KiB (840.4 KiB/s) with 12 file(s) remaining\rCompleted 234.0 KiB/843.4 KiB (1.5 MiB/s) with 12 file(s) remaining  \rupload: contents/BIOMD0000000687.vcml to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/BIOMD0000000687.vcml\nCompleted 234.0 KiB/843.4 KiB (1.5 MiB/s) with 11 file(s) remaining\rCompleted 332.6 KiB/843.4 KiB (2.1 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000687_url.xml to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/BIOMD0000000687_url.xml\nCompleted 332.6 KiB/843.4 KiB (2.1 MiB/s) with 10 file(s) remaining\rCompleted 338.2 KiB/843.4 KiB (2.0 MiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/metadata.rdf\nCompleted 338.2 KiB/843.4 KiB (2.0 MiB/s) with 9 file(s) remaining\rCompleted 452.1 KiB/843.4 KiB (2.6 MiB/s) with 9 file(s) remaining\rupload: contents/MODEL1006230052.cps to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/MODEL1006230052.cps\nCompleted 452.1 KiB/843.4 KiB (2.6 MiB/s) with 8 file(s) remaining\rCompleted 454.0 KiB/843.4 KiB (2.6 MiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/manifest.xml\nCompleted 454.0 KiB/843.4 KiB (2.6 MiB/s) with 7 file(s) remaining\rCompleted 454.1 KiB/843.4 KiB (2.5 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/curation_notes.txt\nCompleted 454.1 KiB/843.4 KiB (2.5 MiB/s) with 6 file(s) remaining\rCompleted 528.3 KiB/843.4 KiB (2.6 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000687.png to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/BIOMD0000000687.png\nCompleted 528.3 KiB/843.4 KiB (2.6 MiB/s) with 5 file(s) remaining\rCompleted 581.0 KiB/843.4 KiB (2.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000687.svg to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/BIOMD0000000687.svg\nCompleted 581.0 KiB/843.4 KiB (2.8 MiB/s) with 4 file(s) remaining\rCompleted 613.8 KiB/843.4 KiB (3.0 MiB/s) with 4 file(s) remaining\rupload: contents/MODEL1006230052.sedml to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/MODEL1006230052.sedml\nCompleted 613.8 KiB/843.4 KiB (3.0 MiB/s) with 3 file(s) remaining\rCompleted 621.1 KiB/843.4 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000687.ode to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/BIOMD0000000687.ode\nCompleted 621.1 KiB/843.4 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 638.5 KiB/843.4 KiB (2.5 MiB/s) with 2 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/curation_image.png\nCompleted 638.5 KiB/843.4 KiB (2.5 MiB/s) with 1 file(s) remaining\rCompleted 843.4 KiB/843.4 KiB (3.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000687.pdf to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/contents/BIOMD0000000687.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.7 KiB/8.7 KiB (86.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c360dcacb55678cc39d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /MODEL1006230052.sedml\ncreating dataset /MODEL1006230052.sedml/autogen_report_for_task1, shape: (58, 701), type: float64\ndataset created, uuid: d-9c9eda9c-8d195238-e6a9-1e7d24-64eaf0, chunk_size: (58, 701)\ncreating dataset /MODEL1006230052.sedml/plot_1_task1, shape: (2, 701), type: float64\ndataset created, uuid: d-9c9eda9c-8d195238-5f7f-0c5888-9aa8c8, chunk_size: (2, 701)\ncreating attribute combineArchiveLocation in /MODEL1006230052.sedml\ncreating attribute uri in /MODEL1006230052.sedml\ncreating attribute _type in /MODEL1006230052.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1006230052.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /MODEL1006230052.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /MODEL1006230052.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /MODEL1006230052.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /MODEL1006230052.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /MODEL1006230052.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /MODEL1006230052.sedml/autogen_report_for_task1\ncreating attribute uri in /MODEL1006230052.sedml/autogen_report_for_task1\ncreating attribute _type in /MODEL1006230052.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1006230052.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /MODEL1006230052.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /MODEL1006230052.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /MODEL1006230052.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /MODEL1006230052.sedml/plot_1_task1\ncreating attribute sedmlId in /MODEL1006230052.sedml/plot_1_task1\ncreating attribute sedmlName in /MODEL1006230052.sedml/plot_1_task1\ncreating attribute uri in /MODEL1006230052.sedml/plot_1_task1\ncreate_links: /\ngot link: MODEL1006230052.sedml\ncreate_links: /MODEL1006230052.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /MODEL1006230052.sedml/autogen_report_for_task1 to tgt: /MODEL1006230052.sedml/autogen_report_for_task1, shape: (58, 701), type: float64\niterating over chunks for /MODEL1006230052.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 58, 1), slice(0, 701, 1))\ndone with dataload for /MODEL1006230052.sedml/autogen_report_for_task1\nwrite_dataset src: /MODEL1006230052.sedml/plot_1_task1 to tgt: /MODEL1006230052.sedml/plot_1_task1, shape: (2, 701), type: float64\niterating over chunks for /MODEL1006230052.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 701, 1))\ndone with dataload for /MODEL1006230052.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c360dcacb55678cc39d\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.\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.739614,"sedDocuments":[{"location":"MODEL1006230052.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  MODEL1006230052.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 58 data sets\r\n    Plots (1):\r\n      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: MODEL1006230052.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":1.188557,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.288896,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.375866,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.329822,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_z_a","status":"SUCCEEDED"},{"id":"autogen_task1_x_0","status":"SUCCEEDED"},{"id":"autogen_task1_y_0","status":"SUCCEEDED"},{"id":"autogen_task1_y_1","status":"SUCCEEDED"},{"id":"autogen_task1_L_0","status":"SUCCEEDED"},{"id":"autogen_task1_v_0","status":"SUCCEEDED"},{"id":"autogen_task1_m_0_0","status":"SUCCEEDED"},{"id":"autogen_task1_m_1_0","status":"SUCCEEDED"},{"id":"autogen_task1_m_2_0","status":"SUCCEEDED"},{"id":"autogen_task1_m_3_0","status":"SUCCEEDED"},{"id":"autogen_task1_m_4_0","status":"SUCCEEDED"},{"id":"autogen_task1_m_5_0","status":"SUCCEEDED"},{"id":"autogen_task1_m_6_0","status":"SUCCEEDED"},{"id":"autogen_task1_m_7_0","status":"SUCCEEDED"},{"id":"autogen_task1_m_8_0","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_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"}]}]}]}