{"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    436      0 --:--:-- --:--:-- --:--:--   437\n\r100 50540  100 50540    0     0   115k      0 --:--:-- --:--:-- --:--:--  115k\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 (26.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/rawLog.txt\nCompleted 5.9 KiB/5.9 KiB (86.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/Andersen2017.sedml/ (stored 0%)\n  adding: outputs/Andersen2017.sedml/plot_2_task1.pdf (deflated 29%)\n  adding: outputs/Andersen2017.sedml/plot_1_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/282.2 KiB (5.7 MiB/s) with 1 file(s) remaining\rCompleted 282.2 KiB/282.2 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/outputs/reports.h5\nCompleted 256.0 KiB/306.6 KiB (6.0 MiB/s) with 5 file(s) remaining\rCompleted 263.0 KiB/306.6 KiB (3.0 MiB/s) with 5 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/output.zip\nCompleted 263.0 KiB/306.6 KiB (3.0 MiB/s) with 4 file(s) remaining\rCompleted 275.4 KiB/306.6 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: outputs/Andersen2017.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/outputs/Andersen2017.sedml/plot_1_task1.pdf\nCompleted 275.4 KiB/306.6 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 287.2 KiB/306.6 KiB (2.4 MiB/s) with 3 file(s) remaining\rupload: outputs/Andersen2017.sedml/plot_2_task1.pdf to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/outputs/Andersen2017.sedml/plot_2_task1.pdf\nCompleted 287.2 KiB/306.6 KiB (2.4 MiB/s) with 2 file(s) remaining\rCompleted 303.8 KiB/306.6 KiB (2.4 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/outputs/plots.zip\nCompleted 303.8 KiB/306.6 KiB (2.4 MiB/s) with 1 file(s) remaining\rCompleted 306.6 KiB/306.6 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Andersen2017-biopax2.owl  \n  inflating: contents/Andersen2017-biopax3.owl  \n  inflating: contents/Andersen2017-matlab.m  \n  inflating: contents/Andersen2017-octave.m  \n  inflating: contents/Andersen2017.cps  \n  inflating: contents/Andersen2017.sedml  \n  inflating: contents/Andersen2017.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 28.1 KiB/310.0 KiB (415.8 KiB/s) with 11 file(s) remaining\rupload: contents/Andersen2017-biopax3.owl to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/Andersen2017-biopax3.owl\nCompleted 28.1 KiB/310.0 KiB (415.8 KiB/s) with 10 file(s) remaining\rCompleted 37.7 KiB/310.0 KiB (368.9 KiB/s) with 10 file(s) remaining\rupload: contents/Andersen2017-matlab.m to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/Andersen2017-matlab.m\nCompleted 37.7 KiB/310.0 KiB (368.9 KiB/s) with 9 file(s) remaining\rCompleted 56.6 KiB/310.0 KiB (457.6 KiB/s) with 9 file(s) remaining\rupload: contents/Andersen2017-biopax2.owl to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/Andersen2017-biopax2.owl\nCompleted 56.6 KiB/310.0 KiB (457.6 KiB/s) with 8 file(s) remaining\rCompleted 56.7 KiB/310.0 KiB (445.0 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/curation_notes.txt\nCompleted 56.7 KiB/310.0 KiB (445.0 KiB/s) with 7 file(s) remaining\rCompleted 58.0 KiB/310.0 KiB (436.1 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/manifest.xml\nCompleted 58.0 KiB/310.0 KiB (436.1 KiB/s) with 6 file(s) remaining\rCompleted 67.7 KiB/310.0 KiB (490.5 KiB/s) with 6 file(s) remaining\rupload: contents/Andersen2017-octave.m to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/Andersen2017-octave.m\nCompleted 67.7 KiB/310.0 KiB (490.5 KiB/s) with 5 file(s) remaining\rCompleted 142.0 KiB/310.0 KiB (952.1 KiB/s) with 5 file(s) remaining\rupload: contents/Andersen2017.xml to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/Andersen2017.xml\nCompleted 142.0 KiB/310.0 KiB (952.1 KiB/s) with 4 file(s) remaining\rCompleted 144.2 KiB/310.0 KiB (894.7 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/metadata.rdf\nCompleted 144.2 KiB/310.0 KiB (894.7 KiB/s) with 3 file(s) remaining\rCompleted 168.6 KiB/310.0 KiB (1.0 MiB/s) with 3 file(s) remaining  \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/curation_image.png\nCompleted 168.6 KiB/310.0 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 200.9 KiB/310.0 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: contents/Andersen2017.sedml to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/Andersen2017.sedml\nCompleted 200.9 KiB/310.0 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 310.0 KiB/310.0 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/Andersen2017.cps to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/contents/Andersen2017.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.6 KiB/7.6 KiB (113.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f17a6262268786a36262/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Andersen2017.sedml\ncreating dataset /Andersen2017.sedml/autogen_report_for_task1, shape: (58, 1001), type: float64\ndataset created, uuid: d-867a9d5d-3c54b066-b5e9-f9b384-418051, chunk_size: (58, 1001)\ncreating dataset /Andersen2017.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-867a9d5d-3c54b066-0a55-eacc9e-bd01fe, chunk_size: (4, 1001)\ncreating dataset /Andersen2017.sedml/plot_2_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-867a9d5d-3c54b066-6f41-64804a-978771, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /Andersen2017.sedml\ncreating attribute uri in /Andersen2017.sedml\ncreating attribute _type in /Andersen2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Andersen2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Andersen2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Andersen2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Andersen2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Andersen2017.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Andersen2017.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Andersen2017.sedml/autogen_report_for_task1\ncreating attribute uri in /Andersen2017.sedml/autogen_report_for_task1\ncreating attribute _type in /Andersen2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Andersen2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Andersen2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Andersen2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Andersen2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Andersen2017.sedml/plot_1_task1\ncreating attribute sedmlId in /Andersen2017.sedml/plot_1_task1\ncreating attribute sedmlName in /Andersen2017.sedml/plot_1_task1\ncreating attribute uri in /Andersen2017.sedml/plot_1_task1\ncreating attribute _type in /Andersen2017.sedml/plot_2_task1\ncreating attribute sedmlDataSetDataTypes in /Andersen2017.sedml/plot_2_task1\ncreating attribute sedmlDataSetIds in /Andersen2017.sedml/plot_2_task1\ncreating attribute sedmlDataSetLabels in /Andersen2017.sedml/plot_2_task1\ncreating attribute sedmlDataSetNames in /Andersen2017.sedml/plot_2_task1\ncreating attribute sedmlDataSetShapes in /Andersen2017.sedml/plot_2_task1\ncreating attribute sedmlId in /Andersen2017.sedml/plot_2_task1\ncreating attribute sedmlName in /Andersen2017.sedml/plot_2_task1\ncreating attribute uri in /Andersen2017.sedml/plot_2_task1\ncreate_links: /\ngot link: Andersen2017.sedml\ncreate_links: /Andersen2017.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ngot link: plot_2_task1\nwrite_dataset src: /Andersen2017.sedml/autogen_report_for_task1 to tgt: /Andersen2017.sedml/autogen_report_for_task1, shape: (58, 1001), type: float64\niterating over chunks for /Andersen2017.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 58, 1), slice(0, 1001, 1))\ndone with dataload for /Andersen2017.sedml/autogen_report_for_task1\nwrite_dataset src: /Andersen2017.sedml/plot_1_task1 to tgt: /Andersen2017.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /Andersen2017.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Andersen2017.sedml/plot_1_task1\nwrite_dataset src: /Andersen2017.sedml/plot_2_task1 to tgt: /Andersen2017.sedml/plot_2_task1, shape: (4, 1001), type: float64\niterating over chunks for /Andersen2017.sedml/plot_2_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Andersen2017.sedml/plot_2_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f17a6262268786a36262\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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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":2.067019,"sedDocuments":[{"location":"Andersen2017.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  Andersen2017.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 58 data sets\r\n    Plots (2):\r\n      plot_1_task1: 3 curves\r\n      plot_2_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Andersen2017.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":1.558163,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.272231,"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":0.424671,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"plot_2_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.215948,"curves":[{"id":"p2_curve_1_task1","status":"SUCCEEDED"},{"id":"p2_curve_2_task1","status":"SUCCEEDED"},{"id":"p2_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.435161,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x0_e4","status":"SUCCEEDED"},{"id":"autogen_task1_x0_y0","status":"SUCCEEDED"},{"id":"autogen_task1_y0_e4","status":"SUCCEEDED"},{"id":"autogen_task1_x1_e10","status":"SUCCEEDED"},{"id":"autogen_task1_x1_y1","status":"SUCCEEDED"},{"id":"autogen_task1_y1_e10","status":"SUCCEEDED"},{"id":"autogen_task1_x0","status":"SUCCEEDED"},{"id":"autogen_task1_x1","status":"SUCCEEDED"},{"id":"autogen_task1_y0","status":"SUCCEEDED"},{"id":"autogen_task1_y1","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_s","status":"SUCCEEDED"},{"id":"autogen_task1_rx","status":"SUCCEEDED"},{"id":"autogen_task1_ax","status":"SUCCEEDED"},{"id":"autogen_task1_Ax","status":"SUCCEEDED"},{"id":"autogen_task1_dx0","status":"SUCCEEDED"},{"id":"autogen_task1_dx1","status":"SUCCEEDED"},{"id":"autogen_task1_cxx","status":"SUCCEEDED"},{"id":"autogen_task1_cxy","status":"SUCCEEDED"},{"id":"autogen_task1_es","status":"SUCCEEDED"},{"id":"autogen_task1_rm","status":"SUCCEEDED"},{"id":"autogen_task1_inflammation","status":"SUCCEEDED"},{"id":"autogen_task1_ry","status":"SUCCEEDED"},{"id":"autogen_task1_ay","status":"SUCCEEDED"},{"id":"autogen_task1_Ay","status":"SUCCEEDED"},{"id":"autogen_task1_dy0","status":"SUCCEEDED"},{"id":"autogen_task1_dy1","status":"SUCCEEDED"},{"id":"autogen_task1_cyx","status":"SUCCEEDED"},{"id":"autogen_task1_cyy","status":"SUCCEEDED"},{"id":"autogen_task1_rs","status":"SUCCEEDED"},{"id":"autogen_task1_ea","status":"SUCCEEDED"},{"id":"autogen_task1_psi_x","status":"SUCCEEDED"},{"id":"autogen_task1_psi_y","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_2","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_1","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_5","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_6","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_15","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_16","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_3","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_4","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_HSC_Self_Renewal","status":"SUCCEEDED"},{"id":"autogen_task1_HSC_Death","status":"SUCCEEDED"},{"id":"autogen_task1_HSC_Proliferation","status":"SUCCEEDED"},{"id":"autogen_task1_HSC_MPN_Mutation","status":"SUCCEEDED"},{"id":"autogen_task1_HSC_Proliferation_HMC","status":"SUCCEEDED"},{"id":"autogen_task1_HMC_Death","status":"SUCCEEDED"},{"id":"autogen_task1_MPN_SC_Self_Renewal","status":"SUCCEEDED"},{"id":"autogen_task1_MPN_SC_Death","status":"SUCCEEDED"},{"id":"autogen_task1_MPN_SC_Proliferation","status":"SUCCEEDED"},{"id":"autogen_task1_MPN_SC_Proliferation_MPN_MC","status":"SUCCEEDED"},{"id":"autogen_task1_MPN_MC_Death","status":"SUCCEEDED"},{"id":"autogen_task1_Dead_Cells_Elimination_Per_Cytokine","status":"SUCCEEDED"},{"id":"autogen_task1_Phagocyte_Upregulation_Dead_Cells","status":"SUCCEEDED"},{"id":"autogen_task1_Cytokine_Elimination","status":"SUCCEEDED"},{"id":"autogen_task1_Cytokines_Inflammation","status":"SUCCEEDED"}]}]}]}