{"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 --:--:--  0:00:01 --:--:--     0\r  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0\r100   139  100   139    0     0     48      0  0:00:02  0:00:02 --:--:--    48\n\r  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0\r100  473k  100  473k    0     0   159k      0  0:00:02  0:00:02 --:--:-- 4734k\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 1.8 KiB/1.8 KiB (27.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/rawLog.txt\nCompleted 3.8 KiB/3.8 KiB (57.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/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 46%)\n  adding: outputs/Perelson1993.sedml/ (stored 0%)\n  adding: outputs/Perelson1993.sedml/plot_1_task1.pdf (deflated 30%)\n  adding: rawLog.txt (deflated 73%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 43.2 KiB/43.2 KiB (538.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/outputs/reports.h5\nCompleted 34.0 KiB/56.2 KiB (469.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/output.zip\nCompleted 34.0 KiB/56.2 KiB (469.6 KiB/s) with 3 file(s) remaining\rCompleted 45.5 KiB/56.2 KiB (437.9 KiB/s) with 3 file(s) remaining\rupload: outputs/Perelson1993.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/outputs/Perelson1993.sedml/plot_1_task1.pdf\nCompleted 45.5 KiB/56.2 KiB (437.9 KiB/s) with 2 file(s) remaining\rCompleted 53.4 KiB/56.2 KiB (456.2 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/outputs/plots.zip\nCompleted 53.4 KiB/56.2 KiB (456.2 KiB/s) with 1 file(s) remaining\rCompleted 56.2 KiB/56.2 KiB (469.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/MODEL1006230079-biopax2.owl  \n  inflating: contents/MODEL1006230079-biopax3.owl  \n  inflating: contents/MODEL1006230079-matlab.m  \n  inflating: contents/MODEL1006230079-octave.m  \n  inflating: contents/MODEL1006230079.m  \n  inflating: contents/MODEL1006230079.ode  \n  inflating: contents/MODEL1006230079.pdf  \n  inflating: contents/MODEL1006230079.png  \n  inflating: contents/MODEL1006230079.svg  \n  inflating: contents/MODEL1006230079_url.xml  \n  inflating: contents/Perelson1993-biopax2.owl  \n  inflating: contents/Perelson1993-biopax3.owl  \n  inflating: contents/Perelson1993-matlab.m  \n  inflating: contents/Perelson1993-octave.m  \n  inflating: contents/Perelson1993.cps  \n  inflating: contents/Perelson1993.ode  \n  inflating: contents/Perelson1993.sedml  \n  inflating: contents/Perelson1993.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 3.4 KiB/751.6 KiB (52.3 KiB/s) with 22 file(s) remaining\rupload: contents/MODEL1006230079-biopax3.owl to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/MODEL1006230079-biopax3.owl\nCompleted 3.4 KiB/751.6 KiB (52.3 KiB/s) with 21 file(s) remaining\rCompleted 7.1 KiB/751.6 KiB (59.4 KiB/s) with 21 file(s) remaining\rupload: contents/MODEL1006230079-matlab.m to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/MODEL1006230079-matlab.m\nCompleted 7.1 KiB/751.6 KiB (59.4 KiB/s) with 20 file(s) remaining\rCompleted 7.9 KiB/751.6 KiB (62.4 KiB/s) with 20 file(s) remaining\rupload: contents/MODEL1006230079.svg to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/MODEL1006230079.svg\nCompleted 7.9 KiB/751.6 KiB (62.4 KiB/s) with 19 file(s) remaining\rCompleted 14.2 KiB/751.6 KiB (110.4 KiB/s) with 19 file(s) remaining\rupload: contents/Perelson1993-octave.m to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/Perelson1993-octave.m\nCompleted 14.2 KiB/751.6 KiB (110.4 KiB/s) with 18 file(s) remaining\rCompleted 17.9 KiB/751.6 KiB (137.7 KiB/s) with 18 file(s) remaining\rupload: contents/MODEL1006230079-octave.m to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/MODEL1006230079-octave.m\nCompleted 17.9 KiB/751.6 KiB (137.7 KiB/s) with 17 file(s) remaining\rCompleted 21.2 KiB/751.6 KiB (155.4 KiB/s) with 17 file(s) remaining\rupload: contents/MODEL1006230079-biopax2.owl to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/MODEL1006230079-biopax2.owl\nCompleted 21.2 KiB/751.6 KiB (155.4 KiB/s) with 16 file(s) remaining\rCompleted 34.8 KiB/751.6 KiB (233.5 KiB/s) with 16 file(s) remaining\rupload: contents/MODEL1006230079_url.xml to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/MODEL1006230079_url.xml\nCompleted 34.8 KiB/751.6 KiB (233.5 KiB/s) with 15 file(s) remaining\rCompleted 45.0 KiB/751.6 KiB (299.2 KiB/s) with 15 file(s) remaining\rupload: contents/Perelson1993-biopax2.owl to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/Perelson1993-biopax2.owl\nCompleted 45.0 KiB/751.6 KiB (299.2 KiB/s) with 14 file(s) remaining\rCompleted 59.9 KiB/751.6 KiB (370.4 KiB/s) with 14 file(s) remaining\rupload: contents/Perelson1993-biopax3.owl to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/Perelson1993-biopax3.owl\nCompleted 59.9 KiB/751.6 KiB (370.4 KiB/s) with 13 file(s) remaining\rCompleted 315.9 KiB/751.6 KiB (1.9 MiB/s) with 13 file(s) remaining \rCompleted 320.2 KiB/751.6 KiB (1.8 MiB/s) with 13 file(s) remaining \rupload: contents/Perelson1993.ode to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/Perelson1993.ode\nCompleted 320.2 KiB/751.6 KiB (1.8 MiB/s) with 12 file(s) remaining\rCompleted 320.4 KiB/751.6 KiB (1.6 MiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/curation_notes.txt\nCompleted 320.4 KiB/751.6 KiB (1.6 MiB/s) with 11 file(s) remaining\rCompleted 335.7 KiB/751.6 KiB (1.6 MiB/s) with 11 file(s) remaining\rupload: contents/Perelson1993.sedml to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/Perelson1993.sedml\nCompleted 335.7 KiB/751.6 KiB (1.6 MiB/s) with 10 file(s) remaining\rCompleted 338.2 KiB/751.6 KiB (1.6 MiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/manifest.xml\nCompleted 338.2 KiB/751.6 KiB (1.6 MiB/s) with 9 file(s) remaining\rCompleted 344.5 KiB/751.6 KiB (1.6 MiB/s) with 9 file(s) remaining\rupload: contents/Perelson1993-matlab.m to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/Perelson1993-matlab.m\nCompleted 344.5 KiB/751.6 KiB (1.6 MiB/s) with 8 file(s) remaining\rCompleted 418.5 KiB/751.6 KiB (1.9 MiB/s) with 8 file(s) remaining\rupload: contents/Perelson1993.cps to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/Perelson1993.cps\nCompleted 418.5 KiB/751.6 KiB (1.9 MiB/s) with 7 file(s) remaining\rCompleted 461.6 KiB/751.6 KiB (2.0 MiB/s) with 7 file(s) remaining\rupload: contents/Perelson1993.xml to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/Perelson1993.xml\nCompleted 461.6 KiB/751.6 KiB (2.0 MiB/s) with 6 file(s) remaining\rCompleted 594.2 KiB/751.6 KiB (2.5 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/curation_image.png\nCompleted 594.2 KiB/751.6 KiB (2.5 MiB/s) with 5 file(s) remaining\rCompleted 600.6 KiB/751.6 KiB (2.5 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/metadata.rdf\nCompleted 600.6 KiB/751.6 KiB (2.5 MiB/s) with 4 file(s) remaining\rCompleted 741.8 KiB/751.6 KiB (3.0 MiB/s) with 4 file(s) remaining\rCompleted 746.8 KiB/751.6 KiB (3.0 MiB/s) with 4 file(s) remaining\rupload: contents/MODEL1006230079.png to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/MODEL1006230079.png\nCompleted 746.8 KiB/751.6 KiB (3.0 MiB/s) with 3 file(s) remaining\rupload: contents/MODEL1006230079.pdf to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/MODEL1006230079.pdf\nCompleted 746.8 KiB/751.6 KiB (3.0 MiB/s) with 2 file(s) remaining\rCompleted 748.6 KiB/751.6 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: contents/MODEL1006230079.ode to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/MODEL1006230079.ode\nCompleted 748.6 KiB/751.6 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 751.6 KiB/751.6 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: contents/MODEL1006230079.m to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/contents/MODEL1006230079.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 10.9 KiB/10.9 KiB (148.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f17cda4ff2037f59c1eb/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Perelson1993.sedml\ncreating dataset /Perelson1993.sedml/autogen_report_for_task1, shape: (24, 151), type: float64\ndataset created, uuid: d-1b0a7f38-14b57469-5c5a-f269fe-fc2df5, chunk_size: (24, 151)\ncreating dataset /Perelson1993.sedml/plot_1_task1, shape: (6, 151), type: float64\ndataset created, uuid: d-1b0a7f38-14b57469-eb92-cb4189-8b85c7, chunk_size: (6, 151)\ncreating attribute combineArchiveLocation in /Perelson1993.sedml\ncreating attribute uri in /Perelson1993.sedml\ncreating attribute _type in /Perelson1993.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Perelson1993.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Perelson1993.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Perelson1993.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Perelson1993.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Perelson1993.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Perelson1993.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Perelson1993.sedml/autogen_report_for_task1\ncreating attribute uri in /Perelson1993.sedml/autogen_report_for_task1\ncreating attribute _type in /Perelson1993.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Perelson1993.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Perelson1993.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Perelson1993.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Perelson1993.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Perelson1993.sedml/plot_1_task1\ncreating attribute sedmlId in /Perelson1993.sedml/plot_1_task1\ncreating attribute sedmlName in /Perelson1993.sedml/plot_1_task1\ncreating attribute uri in /Perelson1993.sedml/plot_1_task1\ncreate_links: /\ngot link: Perelson1993.sedml\ncreate_links: /Perelson1993.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Perelson1993.sedml/autogen_report_for_task1 to tgt: /Perelson1993.sedml/autogen_report_for_task1, shape: (24, 151), type: float64\niterating over chunks for /Perelson1993.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 24, 1), slice(0, 151, 1))\ndone with dataload for /Perelson1993.sedml/autogen_report_for_task1\nwrite_dataset src: /Perelson1993.sedml/plot_1_task1 to tgt: /Perelson1993.sedml/plot_1_task1, shape: (6, 151), type: float64\niterating over chunks for /Perelson1993.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 151, 1))\ndone with dataload for /Perelson1993.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f17cda4ff2037f59c1eb\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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.076978,"sedDocuments":[{"location":"Perelson1993.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  Perelson1993.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 24 data sets\r\n    Plots (1):\r\n      plot_1_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: Perelson1993.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":0.689976,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.189274,"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":0.315548,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"},{"id":"p1_curve_4_task1","status":"SUCCEEDED"},{"id":"p1_curve_5_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.072404,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_T_1","status":"SUCCEEDED"},{"id":"autogen_task1_T_2","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_T_tot","status":"SUCCEEDED"},{"id":"autogen_task1_s","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_T_max","status":"SUCCEEDED"},{"id":"autogen_task1_mu_T","status":"SUCCEEDED"},{"id":"autogen_task1_k_1","status":"SUCCEEDED"},{"id":"autogen_task1_k_2","status":"SUCCEEDED"},{"id":"autogen_task1_mu_b","status":"SUCCEEDED"},{"id":"autogen_task1_mu_V","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_COMpartment","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_CD4__T_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Death_of_CD4__T_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_Latently_infected_T_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Death_of_Latently_infected_T_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_Actively_infected_T_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Death_of_Actively_infected_T_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Production_of_infectious_virus_particle","status":"SUCCEEDED"},{"id":"autogen_task1_Death_of_infectious_virus_particle","status":"SUCCEEDED"}]}]}]}