{"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    456      0 --:--:-- --:--:-- --:--:--   457\n\r100  357k  100  357k    0     0   819k      0 --:--:-- --:--:-- --:--:--  819k\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 (25.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (48.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/Sandip2013.sedml/ (stored 0%)\n  adding: outputs/Sandip2013.sedml/plot_1_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 57%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 35.2 KiB/35.2 KiB (484.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/outputs/reports.h5\nCompleted 25.7 KiB/47.7 KiB (308.1 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/output.zip\nCompleted 25.7 KiB/47.7 KiB (308.1 KiB/s) with 3 file(s) remaining\rCompleted 33.8 KiB/47.7 KiB (311.9 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/outputs/plots.zip\nCompleted 33.8 KiB/47.7 KiB (311.9 KiB/s) with 2 file(s) remaining\rCompleted 45.1 KiB/47.7 KiB (393.3 KiB/s) with 2 file(s) remaining\rupload: outputs/Sandip2013.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/outputs/Sandip2013.sedml/plot_1_task1.pdf\nCompleted 45.1 KiB/47.7 KiB (393.3 KiB/s) with 1 file(s) remaining\rCompleted 47.7 KiB/47.7 KiB (364.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Sandip2013-biopax2.owl  \n  inflating: contents/Sandip2013-biopax3.owl  \n  inflating: contents/Sandip2013-matlab.m  \n  inflating: contents/Sandip2013-octave.m  \n  inflating: contents/Sandip2013.cps  \n  inflating: contents/Sandip2013.ode  \n  inflating: contents/Sandip2013.sedml  \n  inflating: contents/Sandip2013.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 14.7 KiB/570.6 KiB (189.5 KiB/s) with 12 file(s) remaining\rupload: contents/Sandip2013-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/Sandip2013-biopax3.owl\nCompleted 14.7 KiB/570.6 KiB (189.5 KiB/s) with 11 file(s) remaining\rCompleted 20.8 KiB/570.6 KiB (200.1 KiB/s) with 11 file(s) remaining\rupload: contents/Sandip2013-matlab.m to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/Sandip2013-matlab.m\nCompleted 20.8 KiB/570.6 KiB (200.1 KiB/s) with 10 file(s) remaining\rCompleted 276.8 KiB/570.6 KiB (2.4 MiB/s) with 10 file(s) remaining \rCompleted 287.1 KiB/570.6 KiB (2.4 MiB/s) with 10 file(s) remaining \rupload: contents/Sandip2013-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/Sandip2013-biopax2.owl\nCompleted 287.1 KiB/570.6 KiB (2.4 MiB/s) with 9 file(s) remaining\rCompleted 293.1 KiB/570.6 KiB (2.3 MiB/s) with 9 file(s) remaining\rupload: contents/Sandip2013-octave.m to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/Sandip2013-octave.m\nCompleted 293.1 KiB/570.6 KiB (2.3 MiB/s) with 8 file(s) remaining\rCompleted 308.3 KiB/570.6 KiB (2.2 MiB/s) with 8 file(s) remaining\rupload: contents/Sandip2013.sedml to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/Sandip2013.sedml\nCompleted 308.3 KiB/570.6 KiB (2.2 MiB/s) with 7 file(s) remaining\rCompleted 308.7 KiB/570.6 KiB (2.1 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/curation_notes.txt\nCompleted 308.7 KiB/570.6 KiB (2.1 MiB/s) with 6 file(s) remaining\rCompleted 311.6 KiB/570.6 KiB (1.9 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/metadata.rdf\nCompleted 311.6 KiB/570.6 KiB (1.9 MiB/s) with 5 file(s) remaining\rCompleted 312.9 KiB/570.6 KiB (1.9 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/manifest.xml\nCompleted 312.9 KiB/570.6 KiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 453.3 KiB/570.6 KiB (2.6 MiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/curation_image.png\nCompleted 453.3 KiB/570.6 KiB (2.6 MiB/s) with 3 file(s) remaining\rCompleted 492.6 KiB/570.6 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: contents/Sandip2013.xml to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/Sandip2013.xml\nCompleted 492.6 KiB/570.6 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 496.8 KiB/570.6 KiB (2.6 MiB/s) with 2 file(s) remaining\rupload: contents/Sandip2013.ode to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/Sandip2013.ode\nCompleted 496.8 KiB/570.6 KiB (2.6 MiB/s) with 1 file(s) remaining\rCompleted 570.6 KiB/570.6 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: contents/Sandip2013.cps to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/contents/Sandip2013.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.4 KiB/7.4 KiB (105.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b7a0fb37cdb9ae737f3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Sandip2013.sedml\ncreating dataset /Sandip2013.sedml/autogen_report_for_task1, shape: (25, 101), type: float64\ndataset created, uuid: d-448a0220-8cbe8bf6-0d78-9da47c-cc21a5, chunk_size: (25, 101)\ncreating dataset /Sandip2013.sedml/plot_1_task1, shape: (5, 101), type: float64\ndataset created, uuid: d-448a0220-8cbe8bf6-b76f-febcbf-2fe1b7, chunk_size: (5, 101)\ncreating attribute combineArchiveLocation in /Sandip2013.sedml\ncreating attribute uri in /Sandip2013.sedml\ncreating attribute _type in /Sandip2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Sandip2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Sandip2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Sandip2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Sandip2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Sandip2013.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Sandip2013.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Sandip2013.sedml/autogen_report_for_task1\ncreating attribute uri in /Sandip2013.sedml/autogen_report_for_task1\ncreating attribute _type in /Sandip2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Sandip2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Sandip2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Sandip2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Sandip2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Sandip2013.sedml/plot_1_task1\ncreating attribute sedmlId in /Sandip2013.sedml/plot_1_task1\ncreating attribute sedmlName in /Sandip2013.sedml/plot_1_task1\ncreating attribute uri in /Sandip2013.sedml/plot_1_task1\ncreate_links: /\ngot link: Sandip2013.sedml\ncreate_links: /Sandip2013.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Sandip2013.sedml/autogen_report_for_task1 to tgt: /Sandip2013.sedml/autogen_report_for_task1, shape: (25, 101), type: float64\niterating over chunks for /Sandip2013.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 25, 1), slice(0, 101, 1))\ndone with dataload for /Sandip2013.sedml/autogen_report_for_task1\nwrite_dataset src: /Sandip2013.sedml/plot_1_task1 to tgt: /Sandip2013.sedml/plot_1_task1, shape: (5, 101), type: float64\niterating over chunks for /Sandip2013.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 101, 1))\ndone with dataload for /Sandip2013.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b7a0fb37cdb9ae737f3\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.\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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":1.061594,"sedDocuments":[{"location":"Sandip2013.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  Sandip2013.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 25 data sets\r\n    Plots (1):\r\n      plot_1_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: Sandip2013.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":0.677509,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.136009,"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":0.34652,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.074941,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_VI","status":"SUCCEEDED"},{"id":"autogen_task1_VNI","status":"SUCCEEDED"},{"id":"autogen_task1_s","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_d1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_d2","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_d3","status":"SUCCEEDED"},{"id":"autogen_task1_nr","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_n1","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_target_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_target_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_infected_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_infected_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_infected_virion","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_infected_virion","status":"SUCCEEDED"},{"id":"autogen_task1_Formation_of_non_infected_virion","status":"SUCCEEDED"},{"id":"autogen_task1_Removal_of_non_infected_virion","status":"SUCCEEDED"}]}]}]}