{"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    430      0 --:--:-- --:--:-- --:--:--   430\n\r 81  375k   81  304k    0     0   544k      0 --:--:-- --:--:-- --:--:--  544k\r100  375k  100  375k    0     0   657k      0 --:--:-- --:--:-- --:--:-- 6461k\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 (25.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/rawLog.txt\nCompleted 3.6 KiB/3.6 KiB (53.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/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/Khajanchi2019.sedml/ (stored 0%)\n  adding: outputs/Khajanchi2019.sedml/plot_1_task1.pdf (deflated 27%)\n  adding: outputs/reports.h5 (deflated 63%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 32.0 KiB/32.0 KiB (417.2 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/outputs/reports.h5\nCompleted 22.8 KiB/45.2 KiB (275.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/output.zip\nCompleted 22.8 KiB/45.2 KiB (275.3 KiB/s) with 3 file(s) remaining\rCompleted 31.0 KiB/45.2 KiB (298.3 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/outputs/plots.zip\nCompleted 31.0 KiB/45.2 KiB (298.3 KiB/s) with 2 file(s) remaining\rCompleted 42.6 KiB/45.2 KiB (368.4 KiB/s) with 2 file(s) remaining\rupload: outputs/Khajanchi2019.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/outputs/Khajanchi2019.sedml/plot_1_task1.pdf\nCompleted 42.6 KiB/45.2 KiB (368.4 KiB/s) with 1 file(s) remaining\rCompleted 45.2 KiB/45.2 KiB (383.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Khajanchi2019-biopax2.owl  \n  inflating: contents/Khajanchi2019-biopax3.owl  \n  inflating: contents/Khajanchi2019-matlab.m  \n  inflating: contents/Khajanchi2019-octave.m  \n  inflating: contents/Khajanchi2019.cps  \n  inflating: contents/Khajanchi2019.ode  \n  inflating: contents/Khajanchi2019.sedml  \n  inflating: contents/Khajanchi2019.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 10.6 KiB/572.4 KiB (154.2 KiB/s) with 12 file(s) remaining\rupload: contents/Khajanchi2019-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/Khajanchi2019-biopax2.owl\nCompleted 10.6 KiB/572.4 KiB (154.2 KiB/s) with 11 file(s) remaining\rCompleted 16.9 KiB/572.4 KiB (148.9 KiB/s) with 11 file(s) remaining\rupload: contents/Khajanchi2019-octave.m to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/Khajanchi2019-octave.m\nCompleted 16.9 KiB/572.4 KiB (148.9 KiB/s) with 10 file(s) remaining\rCompleted 23.1 KiB/572.4 KiB (202.3 KiB/s) with 10 file(s) remaining\rupload: contents/Khajanchi2019-matlab.m to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/Khajanchi2019-matlab.m\nCompleted 23.1 KiB/572.4 KiB (202.3 KiB/s) with 9 file(s) remaining\rCompleted 279.1 KiB/572.4 KiB (2.3 MiB/s) with 9 file(s) remaining \rCompleted 312.1 KiB/572.4 KiB (2.4 MiB/s) with 9 file(s) remaining \rupload: contents/Khajanchi2019.xml to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/Khajanchi2019.xml\nCompleted 312.1 KiB/572.4 KiB (2.4 MiB/s) with 8 file(s) remaining\rCompleted 316.3 KiB/572.4 KiB (2.2 MiB/s) with 8 file(s) remaining\rupload: contents/Khajanchi2019.ode to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/Khajanchi2019.ode\nCompleted 316.3 KiB/572.4 KiB (2.2 MiB/s) with 7 file(s) remaining\rCompleted 316.4 KiB/572.4 KiB (2.2 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/curation_notes.txt\nCompleted 316.4 KiB/572.4 KiB (2.2 MiB/s) with 6 file(s) remaining\rCompleted 331.1 KiB/572.4 KiB (1.9 MiB/s) with 6 file(s) remaining\rupload: contents/Khajanchi2019.sedml to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/Khajanchi2019.sedml\nCompleted 331.1 KiB/572.4 KiB (1.9 MiB/s) with 5 file(s) remaining\rCompleted 335.6 KiB/572.4 KiB (1.9 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/metadata.rdf\nCompleted 335.6 KiB/572.4 KiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 349.9 KiB/572.4 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: contents/Khajanchi2019-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/Khajanchi2019-biopax3.owl\nCompleted 349.9 KiB/572.4 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 512.3 KiB/572.4 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/curation_image.png\nCompleted 512.3 KiB/572.4 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 571.0 KiB/572.4 KiB (3.1 MiB/s) with 2 file(s) remaining\rupload: contents/Khajanchi2019.cps to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/Khajanchi2019.cps\nCompleted 571.0 KiB/572.4 KiB (3.1 MiB/s) with 1 file(s) remaining\rCompleted 572.4 KiB/572.4 KiB (2.9 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.6 KiB/7.6 KiB (109.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b790fb37cdb9ae737e9/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Khajanchi2019.sedml\ncreating dataset /Khajanchi2019.sedml/autogen_report_for_task1, shape: (23, 101), type: float64\ndataset created, uuid: d-9e06e6ab-1cf0c2a0-ca25-ff7823-27fcbe, chunk_size: (23, 101)\ncreating dataset /Khajanchi2019.sedml/plot_1_task1, shape: (4, 101), type: float64\ndataset created, uuid: d-9e06e6ab-1cf0c2a0-be62-f6bcb5-a732c8, chunk_size: (4, 101)\ncreating attribute combineArchiveLocation in /Khajanchi2019.sedml\ncreating attribute uri in /Khajanchi2019.sedml\ncreating attribute _type in /Khajanchi2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Khajanchi2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Khajanchi2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Khajanchi2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Khajanchi2019.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Khajanchi2019.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Khajanchi2019.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Khajanchi2019.sedml/autogen_report_for_task1\ncreating attribute uri in /Khajanchi2019.sedml/autogen_report_for_task1\ncreating attribute _type in /Khajanchi2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Khajanchi2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Khajanchi2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Khajanchi2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Khajanchi2019.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Khajanchi2019.sedml/plot_1_task1\ncreating attribute sedmlId in /Khajanchi2019.sedml/plot_1_task1\ncreating attribute sedmlName in /Khajanchi2019.sedml/plot_1_task1\ncreating attribute uri in /Khajanchi2019.sedml/plot_1_task1\ncreate_links: /\ngot link: Khajanchi2019.sedml\ncreate_links: /Khajanchi2019.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Khajanchi2019.sedml/autogen_report_for_task1 to tgt: /Khajanchi2019.sedml/autogen_report_for_task1, shape: (23, 101), type: float64\niterating over chunks for /Khajanchi2019.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 23, 1), slice(0, 101, 1))\ndone with dataload for /Khajanchi2019.sedml/autogen_report_for_task1\nwrite_dataset src: /Khajanchi2019.sedml/plot_1_task1 to tgt: /Khajanchi2019.sedml/plot_1_task1, shape: (4, 101), type: float64\niterating over chunks for /Khajanchi2019.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 101, 1))\ndone with dataload for /Khajanchi2019.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b790fb37cdb9ae737e9\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 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.\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":1.259687,"sedDocuments":[{"location":"Khajanchi2019.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  Khajanchi2019.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 23 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Khajanchi2019.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":0.81106,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.220131,"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":0.390457,"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":0.071245,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_w","status":"SUCCEEDED"},{"id":"autogen_task1_r_1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_2","status":"SUCCEEDED"},{"id":"autogen_task1_k_1","status":"SUCCEEDED"},{"id":"autogen_task1_r_2","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_3","status":"SUCCEEDED"},{"id":"autogen_task1_k_2","status":"SUCCEEDED"},{"id":"autogen_task1_gamma_1","status":"SUCCEEDED"},{"id":"autogen_task1_k_3","status":"SUCCEEDED"},{"id":"autogen_task1_mu_1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_4","status":"SUCCEEDED"},{"id":"autogen_task1_k_4","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Increase_in_density_of_glioma_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Decrease_in_density_of_glioma_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Increase_in_density_of_macrophage_population","status":"SUCCEEDED"},{"id":"autogen_task1_Decrease_in_the_density_of_macrophage_population","status":"SUCCEEDED"},{"id":"autogen_task1_Increase_in_density_of_glioma_specific_CD8__T_cell","status":"SUCCEEDED"},{"id":"autogen_task1_decrease_in_density_of_glioma_specific_CD8__T_cell","status":"SUCCEEDED"}]}]}]}