{"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    448      0 --:--:-- --:--:-- --:--:--   449\n\r100 47784  100 47784    0     0   114k      0 --:--:-- --:--:-- --:--:--  114k\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 3 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 3\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 (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (22.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/rawLog.txt\nCompleted 4.2 KiB/4.2 KiB (67.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/Jarrett2018.sedml/ (stored 0%)\n  adding: outputs/Jarrett2018.sedml/plot_2_task1.pdf (deflated 30%)\n  adding: outputs/Jarrett2018.sedml/plot_1_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 64%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 53.8 KiB/53.8 KiB (648.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/outputs/reports.h5\nCompleted 41.1 KiB/89.1 KiB (474.6 KiB/s) with 5 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/output.zip\nCompleted 41.1 KiB/89.1 KiB (474.6 KiB/s) with 4 file(s) remaining\rCompleted 59.8 KiB/89.1 KiB (517.4 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/outputs/plots.zip\nCompleted 59.8 KiB/89.1 KiB (517.4 KiB/s) with 3 file(s) remaining\rCompleted 75.6 KiB/89.1 KiB (622.6 KiB/s) with 3 file(s) remaining\rupload: outputs/Jarrett2018.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/outputs/Jarrett2018.sedml/plot_1_task1.pdf\nCompleted 75.6 KiB/89.1 KiB (622.6 KiB/s) with 2 file(s) remaining\rCompleted 86.4 KiB/89.1 KiB (694.7 KiB/s) with 2 file(s) remaining\rupload: outputs/Jarrett2018.sedml/plot_2_task1.pdf to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/outputs/Jarrett2018.sedml/plot_2_task1.pdf\nCompleted 86.4 KiB/89.1 KiB (694.7 KiB/s) with 1 file(s) remaining\rCompleted 89.1 KiB/89.1 KiB (700.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Jarrett2018-biopax2.owl  \n  inflating: contents/Jarrett2018-biopax3.owl  \n  inflating: contents/Jarrett2018-matlab.m  \n  inflating: contents/Jarrett2018-octave.m  \n  inflating: contents/Jarrett2018.cps  \n  inflating: contents/Jarrett2018.ode  \n  inflating: contents/Jarrett2018.sedml  \n  inflating: contents/Jarrett2018.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 14.6 KiB/265.4 KiB (150.3 KiB/s) with 12 file(s) remaining\rupload: contents/Jarrett2018-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/Jarrett2018-biopax2.owl\nCompleted 14.6 KiB/265.4 KiB (150.3 KiB/s) with 11 file(s) remaining\rCompleted 20.4 KiB/265.4 KiB (177.3 KiB/s) with 11 file(s) remaining\rupload: contents/Jarrett2018-octave.m to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/Jarrett2018-octave.m\nCompleted 20.4 KiB/265.4 KiB (177.3 KiB/s) with 10 file(s) remaining\rCompleted 26.1 KiB/265.4 KiB (213.3 KiB/s) with 10 file(s) remaining\rupload: contents/Jarrett2018-matlab.m to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/Jarrett2018-matlab.m\nCompleted 26.1 KiB/265.4 KiB (213.3 KiB/s) with 9 file(s) remaining\rCompleted 101.1 KiB/265.4 KiB (752.0 KiB/s) with 9 file(s) remaining\rupload: contents/Jarrett2018.xml to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/Jarrett2018.xml\nCompleted 101.1 KiB/265.4 KiB (752.0 KiB/s) with 8 file(s) remaining\rCompleted 102.5 KiB/265.4 KiB (733.0 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/manifest.xml\nCompleted 102.5 KiB/265.4 KiB (733.0 KiB/s) with 7 file(s) remaining\rCompleted 102.7 KiB/265.4 KiB (724.4 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/curation_notes.txt\nCompleted 102.7 KiB/265.4 KiB (724.4 KiB/s) with 6 file(s) remaining\rCompleted 107.1 KiB/265.4 KiB (685.9 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/metadata.rdf\nCompleted 107.1 KiB/265.4 KiB (685.9 KiB/s) with 5 file(s) remaining\rCompleted 126.5 KiB/265.4 KiB (798.9 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/curation_image.png\nCompleted 126.5 KiB/265.4 KiB (798.9 KiB/s) with 4 file(s) remaining\rCompleted 144.3 KiB/265.4 KiB (790.2 KiB/s) with 4 file(s) remaining\rupload: contents/Jarrett2018.sedml to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/Jarrett2018.sedml\nCompleted 144.3 KiB/265.4 KiB (790.2 KiB/s) with 3 file(s) remaining\rCompleted 148.2 KiB/265.4 KiB (801.5 KiB/s) with 3 file(s) remaining\rupload: contents/Jarrett2018.ode to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/Jarrett2018.ode\nCompleted 148.2 KiB/265.4 KiB (801.5 KiB/s) with 2 file(s) remaining\rCompleted 167.7 KiB/265.4 KiB (896.5 KiB/s) with 2 file(s) remaining\rupload: contents/Jarrett2018-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/Jarrett2018-biopax3.owl\nCompleted 167.7 KiB/265.4 KiB (896.5 KiB/s) with 1 file(s) remaining\rCompleted 265.4 KiB/265.4 KiB (1.3 MiB/s) with 1 file(s) remaining  \rupload: contents/Jarrett2018.cps to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/contents/Jarrett2018.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.8 KiB/7.8 KiB (112.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b5a77b6669655061174/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Jarrett2018.sedml\ncreating dataset /Jarrett2018.sedml/autogen_report_for_task1, shape: (30, 101), type: float64\ndataset created, uuid: d-7313e1e1-12e9bbea-4270-c6732b-c548e5, chunk_size: (30, 101)\ncreating dataset /Jarrett2018.sedml/plot_1_task1, shape: (5, 101), type: float64\ndataset created, uuid: d-7313e1e1-12e9bbea-1734-e97136-7984fd, chunk_size: (5, 101)\ncreating dataset /Jarrett2018.sedml/plot_2_task1, shape: (2, 101), type: float64\ndataset created, uuid: d-7313e1e1-12e9bbea-63e0-da1d91-18b424, chunk_size: (2, 101)\ncreating attribute combineArchiveLocation in /Jarrett2018.sedml\ncreating attribute uri in /Jarrett2018.sedml\ncreating attribute _type in /Jarrett2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Jarrett2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Jarrett2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Jarrett2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Jarrett2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Jarrett2018.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Jarrett2018.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Jarrett2018.sedml/autogen_report_for_task1\ncreating attribute uri in /Jarrett2018.sedml/autogen_report_for_task1\ncreating attribute _type in /Jarrett2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Jarrett2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Jarrett2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Jarrett2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Jarrett2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Jarrett2018.sedml/plot_1_task1\ncreating attribute sedmlId in /Jarrett2018.sedml/plot_1_task1\ncreating attribute sedmlName in /Jarrett2018.sedml/plot_1_task1\ncreating attribute uri in /Jarrett2018.sedml/plot_1_task1\ncreating attribute _type in /Jarrett2018.sedml/plot_2_task1\ncreating attribute sedmlDataSetDataTypes in /Jarrett2018.sedml/plot_2_task1\ncreating attribute sedmlDataSetIds in /Jarrett2018.sedml/plot_2_task1\ncreating attribute sedmlDataSetLabels in /Jarrett2018.sedml/plot_2_task1\ncreating attribute sedmlDataSetNames in /Jarrett2018.sedml/plot_2_task1\ncreating attribute sedmlDataSetShapes in /Jarrett2018.sedml/plot_2_task1\ncreating attribute sedmlId in /Jarrett2018.sedml/plot_2_task1\ncreating attribute sedmlName in /Jarrett2018.sedml/plot_2_task1\ncreating attribute uri in /Jarrett2018.sedml/plot_2_task1\ncreate_links: /\ngot link: Jarrett2018.sedml\ncreate_links: /Jarrett2018.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ngot link: plot_2_task1\nwrite_dataset src: /Jarrett2018.sedml/autogen_report_for_task1 to tgt: /Jarrett2018.sedml/autogen_report_for_task1, shape: (30, 101), type: float64\niterating over chunks for /Jarrett2018.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 30, 1), slice(0, 101, 1))\ndone with dataload for /Jarrett2018.sedml/autogen_report_for_task1\nwrite_dataset src: /Jarrett2018.sedml/plot_1_task1 to tgt: /Jarrett2018.sedml/plot_1_task1, shape: (5, 101), type: float64\niterating over chunks for /Jarrett2018.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 101, 1))\ndone with dataload for /Jarrett2018.sedml/plot_1_task1\nwrite_dataset src: /Jarrett2018.sedml/plot_2_task1 to tgt: /Jarrett2018.sedml/plot_2_task1, shape: (2, 101), type: float64\niterating over chunks for /Jarrett2018.sedml/plot_2_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 101, 1))\ndone with dataload for /Jarrett2018.sedml/plot_2_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b5a77b6669655061174\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess 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 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":1.561964,"sedDocuments":[{"location":"Jarrett2018.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 2 plots:\r\n  Jarrett2018.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 30 data sets\r\n    Plots (2):\r\n      plot_1_task1: 4 curves\r\n      plot_2_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: Jarrett2018.sedml ...\r\n  Found 1 tasks and 3 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_task1`\r\n      `plot_2_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 3 outputs ...\r\n      Generating output 1: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_2_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 3: `autogen_report_for_task1` ...","duration":1.071651,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.252165,"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":0.380896,"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":"plot_2_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.171156,"curves":[{"id":"p2_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.081368,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_H","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_g","status":"SUCCEEDED"},{"id":"autogen_task1_an","status":"SUCCEEDED"},{"id":"autogen_task1_av","status":"SUCCEEDED"},{"id":"autogen_task1_ut","status":"SUCCEEDED"},{"id":"autogen_task1_ui","status":"SUCCEEDED"},{"id":"autogen_task1_at","status":"SUCCEEDED"},{"id":"autogen_task1_ai","status":"SUCCEEDED"},{"id":"autogen_task1_uv","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_un","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_rho","status":"SUCCEEDED"},{"id":"autogen_task1_tumor","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_death","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_growth","status":"SUCCEEDED"},{"id":"autogen_task1_immune_stimulation","status":"SUCCEEDED"},{"id":"autogen_task1_immune_inhibition","status":"SUCCEEDED"},{"id":"autogen_task1_vasc_increase","status":"SUCCEEDED"},{"id":"autogen_task1_vasc_decrease","status":"SUCCEEDED"},{"id":"autogen_task1_necrotise","status":"SUCCEEDED"},{"id":"autogen_task1_de_necrotise","status":"SUCCEEDED"},{"id":"autogen_task1_hypoxia","status":"SUCCEEDED"},{"id":"autogen_task1_normoxia","status":"SUCCEEDED"}]}]}]}