{"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    388      0 --:--:-- --:--:-- --:--:--   389\n\r100 51643  100 51643    0     0   101k      0 --:--:-- --:--:-- --:--:--  101k\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 (13.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/rawLog.txt\nCompleted 3.0 KiB/3.0 KiB (26.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/Chen2011_2.sedml/ (stored 0%)\n  adding: outputs/Chen2011_2.sedml/plot_1_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 67%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 29.9 KiB/29.9 KiB (152.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/outputs/reports.h5\nCompleted 20.1 KiB/41.0 KiB (143.8 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/output.zip\nCompleted 20.1 KiB/41.0 KiB (143.8 KiB/s) with 3 file(s) remaining\rCompleted 27.7 KiB/41.0 KiB (159.7 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/outputs/plots.zip\nCompleted 27.7 KiB/41.0 KiB (159.7 KiB/s) with 2 file(s) remaining\rCompleted 30.2 KiB/41.0 KiB (162.5 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/rawLog.txt\nCompleted 30.2 KiB/41.0 KiB (162.5 KiB/s) with 1 file(s) remaining\rCompleted 41.0 KiB/41.0 KiB (189.0 KiB/s) with 1 file(s) remaining\rupload: outputs/Chen2011_2.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/outputs/Chen2011_2.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Chen2011_2-biopax2.owl  \n  inflating: contents/Chen2011_2-biopax3.owl  \n  inflating: contents/Chen2011_2-matlab.m  \n  inflating: contents/Chen2011_2-octave.m  \n  inflating: contents/Chen2011_2.cps  \n  inflating: contents/Chen2011_2.ode  \n  inflating: contents/Chen2011_2.sedml  \n  inflating: contents/Chen2011_2.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 9.3 KiB/177.0 KiB (80.4 KiB/s) with 12 file(s) remaining\rupload: contents/Chen2011_2-biopax2.owl to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/Chen2011_2-biopax2.owl\nCompleted 9.3 KiB/177.0 KiB (80.4 KiB/s) with 11 file(s) remaining\rCompleted 13.1 KiB/177.0 KiB (82.2 KiB/s) with 11 file(s) remaining\rupload: contents/Chen2011_2-matlab.m to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/Chen2011_2-matlab.m\nCompleted 13.1 KiB/177.0 KiB (82.2 KiB/s) with 10 file(s) remaining\rCompleted 51.1 KiB/177.0 KiB (294.3 KiB/s) with 10 file(s) remaining\rupload: contents/Chen2011_2.xml to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/Chen2011_2.xml\nCompleted 51.1 KiB/177.0 KiB (294.3 KiB/s) with 9 file(s) remaining\rCompleted 51.2 KiB/177.0 KiB (271.0 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/curation_notes.txt\nCompleted 51.2 KiB/177.0 KiB (271.0 KiB/s) with 8 file(s) remaining\rCompleted 55.0 KiB/177.0 KiB (287.6 KiB/s) with 8 file(s) remaining\rupload: contents/Chen2011_2-octave.m to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/Chen2011_2-octave.m\nCompleted 55.0 KiB/177.0 KiB (287.6 KiB/s) with 7 file(s) remaining\rCompleted 88.5 KiB/177.0 KiB (457.8 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/curation_image.png\nCompleted 88.5 KiB/177.0 KiB (457.8 KiB/s) with 6 file(s) remaining\rCompleted 89.9 KiB/177.0 KiB (435.4 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/manifest.xml\nCompleted 89.9 KiB/177.0 KiB (435.4 KiB/s) with 5 file(s) remaining\rCompleted 99.8 KiB/177.0 KiB (471.9 KiB/s) with 5 file(s) remaining\rupload: contents/Chen2011_2.sedml to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/Chen2011_2.sedml\nCompleted 99.8 KiB/177.0 KiB (471.9 KiB/s) with 4 file(s) remaining\rCompleted 101.8 KiB/177.0 KiB (474.7 KiB/s) with 4 file(s) remaining\rupload: contents/Chen2011_2.ode to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/Chen2011_2.ode\nCompleted 101.8 KiB/177.0 KiB (474.7 KiB/s) with 3 file(s) remaining\rCompleted 160.6 KiB/177.0 KiB (644.6 KiB/s) with 3 file(s) remaining\rupload: contents/Chen2011_2.cps to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/Chen2011_2.cps\nCompleted 160.6 KiB/177.0 KiB (644.6 KiB/s) with 2 file(s) remaining\rCompleted 164.8 KiB/177.0 KiB (633.5 KiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/metadata.rdf\nCompleted 164.8 KiB/177.0 KiB (633.5 KiB/s) with 1 file(s) remaining\rCompleted 177.0 KiB/177.0 KiB (672.9 KiB/s) with 1 file(s) remaining\rupload: contents/Chen2011_2-biopax3.owl to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/contents/Chen2011_2-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.4 KiB/7.4 KiB (59.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6479328677b6669655038e19/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Chen2011_2.sedml\ncreating dataset /Chen2011_2.sedml/autogen_report_for_task1, shape: (16, 101), type: float64\ndataset created, uuid: d-7f5aa273-155c583d-376f-88bafa-1a2d3d, chunk_size: (16, 101)\ncreating dataset /Chen2011_2.sedml/plot_1_task1, shape: (3, 101), type: float64\ndataset created, uuid: d-7f5aa273-155c583d-2390-f9f5fa-84fe98, chunk_size: (3, 101)\ncreating attribute combineArchiveLocation in /Chen2011_2.sedml\ncreating attribute uri in /Chen2011_2.sedml\ncreating attribute _type in /Chen2011_2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Chen2011_2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Chen2011_2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Chen2011_2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Chen2011_2.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Chen2011_2.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Chen2011_2.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Chen2011_2.sedml/autogen_report_for_task1\ncreating attribute uri in /Chen2011_2.sedml/autogen_report_for_task1\ncreating attribute _type in /Chen2011_2.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Chen2011_2.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Chen2011_2.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Chen2011_2.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Chen2011_2.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Chen2011_2.sedml/plot_1_task1\ncreating attribute sedmlId in /Chen2011_2.sedml/plot_1_task1\ncreating attribute sedmlName in /Chen2011_2.sedml/plot_1_task1\ncreating attribute uri in /Chen2011_2.sedml/plot_1_task1\ncreate_links: /\ngot link: Chen2011_2.sedml\ncreate_links: /Chen2011_2.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Chen2011_2.sedml/autogen_report_for_task1 to tgt: /Chen2011_2.sedml/autogen_report_for_task1, shape: (16, 101), type: float64\niterating over chunks for /Chen2011_2.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 101, 1))\ndone with dataload for /Chen2011_2.sedml/autogen_report_for_task1\nwrite_dataset src: /Chen2011_2.sedml/plot_1_task1 to tgt: /Chen2011_2.sedml/plot_1_task1, shape: (3, 101), type: float64\niterating over chunks for /Chen2011_2.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 101, 1))\ndone with dataload for /Chen2011_2.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6479328677b6669655038e19\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.\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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":0.98487,"sedDocuments":[{"location":"Chen2011_2.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  Chen2011_2.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 16 data sets\r\n    Plots (1):\r\n      plot_1_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Chen2011_2.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":0.631878,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.168422,"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":0.29,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.064722,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_H","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_b1","status":"SUCCEEDED"},{"id":"autogen_task1_u1","status":"SUCCEEDED"},{"id":"autogen_task1_b2","status":"SUCCEEDED"},{"id":"autogen_task1_u2","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_bone_marrow","status":"SUCCEEDED"},{"id":"autogen_task1_HSC_growth","status":"SUCCEEDED"},{"id":"autogen_task1_HSC_death","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_death","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_inhibition","status":"SUCCEEDED"},{"id":"autogen_task1_HSC_inhibition","status":"SUCCEEDED"}]}]}]}