{"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    414      0 --:--:-- --:--:-- --:--:--   414\n\r100 41509  100 41509    0     0  91423      0 --:--:-- --:--:-- --:--:-- 91423\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 (17.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/rawLog.txt\nCompleted 3.4 KiB/3.4 KiB (54.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/Dong2014.sedml/ (stored 0%)\n  adding: outputs/Dong2014.sedml/plot_1_task1.pdf (deflated 15%)\n  adding: outputs/reports.h5 (deflated 18%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 117.1 KiB/117.1 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/outputs/reports.h5\nCompleted 114.9 KiB/152.0 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/output.zip\nCompleted 114.9 KiB/152.0 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 133.7 KiB/152.0 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: outputs/Dong2014.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/outputs/Dong2014.sedml/plot_1_task1.pdf\nCompleted 133.7 KiB/152.0 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 149.4 KiB/152.0 KiB (981.4 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/outputs/plots.zip\nCompleted 149.4 KiB/152.0 KiB (981.4 KiB/s) with 1 file(s) remaining\rCompleted 152.0 KiB/152.0 KiB (979.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Dong2014-biopax2.owl  \n  inflating: contents/Dong2014-biopax3.owl  \n  inflating: contents/Dong2014-matlab.m  \n  inflating: contents/Dong2014-octave.m  \n  inflating: contents/Dong2014.cps   \n  inflating: contents/Dong2014.ode   \n  inflating: contents/Dong2014.sedml  \n  inflating: contents/Dong2014.xml   \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 15.8 KiB/169.1 KiB (224.1 KiB/s) with 12 file(s) remaining\rupload: contents/Dong2014-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/Dong2014-biopax3.owl\nCompleted 15.8 KiB/169.1 KiB (224.1 KiB/s) with 11 file(s) remaining\rCompleted 20.9 KiB/169.1 KiB (187.9 KiB/s) with 11 file(s) remaining\rupload: contents/Dong2014-matlab.m to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/Dong2014-matlab.m\nCompleted 20.9 KiB/169.1 KiB (187.9 KiB/s) with 10 file(s) remaining\rCompleted 32.3 KiB/169.1 KiB (263.5 KiB/s) with 10 file(s) remaining\rupload: contents/Dong2014-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/Dong2014-biopax2.owl\nCompleted 32.3 KiB/169.1 KiB (263.5 KiB/s) with 9 file(s) remaining\rCompleted 35.9 KiB/169.1 KiB (283.7 KiB/s) with 9 file(s) remaining\rupload: contents/Dong2014.ode to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/Dong2014.ode\nCompleted 35.9 KiB/169.1 KiB (283.7 KiB/s) with 8 file(s) remaining\rCompleted 69.4 KiB/169.1 KiB (505.8 KiB/s) with 8 file(s) remaining\rupload: contents/Dong2014.xml to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/Dong2014.xml\nCompleted 69.4 KiB/169.1 KiB (505.8 KiB/s) with 7 file(s) remaining\rCompleted 70.7 KiB/169.1 KiB (455.0 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/manifest.xml\nCompleted 70.7 KiB/169.1 KiB (455.0 KiB/s) with 6 file(s) remaining\rCompleted 91.0 KiB/169.1 KiB (576.8 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/curation_image.png\nCompleted 91.0 KiB/169.1 KiB (576.8 KiB/s) with 5 file(s) remaining\rCompleted 91.2 KiB/169.1 KiB (568.2 KiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/curation_notes.txt\nCompleted 91.2 KiB/169.1 KiB (568.2 KiB/s) with 4 file(s) remaining\rCompleted 96.3 KiB/169.1 KiB (591.5 KiB/s) with 4 file(s) remaining\rupload: contents/Dong2014-octave.m to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/Dong2014-octave.m\nCompleted 96.3 KiB/169.1 KiB (591.5 KiB/s) with 3 file(s) remaining\rCompleted 99.1 KiB/169.1 KiB (573.0 KiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/metadata.rdf\nCompleted 99.1 KiB/169.1 KiB (573.0 KiB/s) with 2 file(s) remaining\rCompleted 112.4 KiB/169.1 KiB (566.8 KiB/s) with 2 file(s) remaining\rupload: contents/Dong2014.sedml to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/Dong2014.sedml\nCompleted 112.4 KiB/169.1 KiB (566.8 KiB/s) with 1 file(s) remaining\rCompleted 169.1 KiB/169.1 KiB (797.8 KiB/s) with 1 file(s) remaining\rupload: contents/Dong2014.cps to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/contents/Dong2014.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.3 KiB/7.3 KiB (101.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b600fb37cdb9ae7363a/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Dong2014.sedml\ncreating dataset /Dong2014.sedml/autogen_report_for_task1, shape: (21, 1001), type: float64\ndataset created, uuid: d-b7d8ed13-0cd6196c-067a-deeb6d-b0991f, chunk_size: (21, 1001)\ncreating dataset /Dong2014.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-b7d8ed13-0cd6196c-375f-659ede-e3a1d9, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /Dong2014.sedml\ncreating attribute uri in /Dong2014.sedml\ncreating attribute _type in /Dong2014.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Dong2014.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Dong2014.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Dong2014.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Dong2014.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Dong2014.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Dong2014.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Dong2014.sedml/autogen_report_for_task1\ncreating attribute uri in /Dong2014.sedml/autogen_report_for_task1\ncreating attribute _type in /Dong2014.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Dong2014.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Dong2014.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Dong2014.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Dong2014.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Dong2014.sedml/plot_1_task1\ncreating attribute sedmlId in /Dong2014.sedml/plot_1_task1\ncreating attribute sedmlName in /Dong2014.sedml/plot_1_task1\ncreating attribute uri in /Dong2014.sedml/plot_1_task1\ncreate_links: /\ngot link: Dong2014.sedml\ncreate_links: /Dong2014.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Dong2014.sedml/autogen_report_for_task1 to tgt: /Dong2014.sedml/autogen_report_for_task1, shape: (21, 1001), type: float64\niterating over chunks for /Dong2014.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 21, 1), slice(0, 1001, 1))\ndone with dataload for /Dong2014.sedml/autogen_report_for_task1\nwrite_dataset src: /Dong2014.sedml/plot_1_task1 to tgt: /Dong2014.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /Dong2014.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Dong2014.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b600fb37cdb9ae7363a\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 and upload the outputs of the simulation run ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.445214,"sedDocuments":[{"location":"Dong2014.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  Dong2014.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 21 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Dong2014.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":0.982102,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.226762,"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":0.434384,"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":0.203425,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x_Tumor_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_y_Effector_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_z_Helper_T_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_delta_1","status":"SUCCEEDED"},{"id":"autogen_task1_omega_1","status":"SUCCEEDED"},{"id":"autogen_task1_sigma_2","status":"SUCCEEDED"},{"id":"autogen_task1_delta_2","status":"SUCCEEDED"},{"id":"autogen_task1_rho","status":"SUCCEEDED"},{"id":"autogen_task1_omega_2","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_Killing_ECs","status":"SUCCEEDED"},{"id":"autogen_task1_EC_Stimulation_Tumor_Debris","status":"SUCCEEDED"},{"id":"autogen_task1_EC_Natural_Death","status":"SUCCEEDED"},{"id":"autogen_task1_EC_Activation_HTC","status":"SUCCEEDED"},{"id":"autogen_task1_HTC_Production","status":"SUCCEEDED"},{"id":"autogen_task1_HTC_Stimulation_Tumor_Antigens","status":"SUCCEEDED"},{"id":"autogen_task1_HTC_Natural_Death","status":"SUCCEEDED"}]}]}]}