{"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    426      0 --:--:-- --:--:-- --:--:--   426\r100   139  100   139    0     0    420      0 --:--:-- --:--:-- --:--:--   419\n\r100 63920  100 63920    0     0   141k      0 --:--:-- --:--:-- --:--:--  141k\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 (24.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/rawLog.txt\nCompleted 4.8 KiB/4.8 KiB (72.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/Yang2012.sedml/ (stored 0%)\n  adding: outputs/Yang2012.sedml/plot_1_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 19%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 136.9 KiB/136.9 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/outputs/reports.h5\nCompleted 121.5 KiB/144.0 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/output.zip\nCompleted 121.5 KiB/144.0 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 133.0 KiB/144.0 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: outputs/Yang2012.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/outputs/Yang2012.sedml/plot_1_task1.pdf\nCompleted 133.0 KiB/144.0 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 135.7 KiB/144.0 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/rawLog.txt\nCompleted 135.7 KiB/144.0 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 144.0 KiB/144.0 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Yang2012-biopax2.owl  \n  inflating: contents/Yang2012-biopax3.owl  \n  inflating: contents/Yang2012-matlab.m  \n  inflating: contents/Yang2012-octave.m  \n  inflating: contents/Yang2012.cps   \n  inflating: contents/Yang2012.ode   \n  inflating: contents/Yang2012.sedml  \n  inflating: contents/Yang2012.xml   \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 6.7 KiB/312.9 KiB (58.8 KiB/s) with 12 file(s) remaining\rupload: contents/Yang2012-octave.m to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/Yang2012-octave.m\nCompleted 6.7 KiB/312.9 KiB (58.8 KiB/s) with 11 file(s) remaining\rCompleted 13.4 KiB/312.9 KiB (106.3 KiB/s) with 11 file(s) remaining\rupload: contents/Yang2012-matlab.m to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/Yang2012-matlab.m\nCompleted 13.4 KiB/312.9 KiB (106.3 KiB/s) with 10 file(s) remaining\rCompleted 103.9 KiB/312.9 KiB (764.9 KiB/s) with 10 file(s) remaining\rupload: contents/Yang2012.xml to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/Yang2012.xml\nCompleted 103.9 KiB/312.9 KiB (764.9 KiB/s) with 9 file(s) remaining\rCompleted 108.5 KiB/312.9 KiB (757.8 KiB/s) with 9 file(s) remaining\rupload: contents/Yang2012.ode to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/Yang2012.ode\nCompleted 108.5 KiB/312.9 KiB (757.8 KiB/s) with 8 file(s) remaining\rCompleted 112.2 KiB/312.9 KiB (763.2 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/metadata.rdf\nCompleted 112.2 KiB/312.9 KiB (763.2 KiB/s) with 7 file(s) remaining\rCompleted 147.8 KiB/312.9 KiB (980.8 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/curation_image.png\nCompleted 147.8 KiB/312.9 KiB (980.8 KiB/s) with 6 file(s) remaining\rCompleted 173.8 KiB/312.9 KiB (1.1 MiB/s) with 6 file(s) remaining  \rupload: contents/Yang2012.sedml to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/Yang2012.sedml\nCompleted 173.8 KiB/312.9 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 173.9 KiB/312.9 KiB (1.0 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/curation_notes.txt\nCompleted 173.9 KiB/312.9 KiB (1.0 MiB/s) with 4 file(s) remaining\rCompleted 175.2 KiB/312.9 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/manifest.xml\nCompleted 175.2 KiB/312.9 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 276.3 KiB/312.9 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/Yang2012.cps to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/Yang2012.cps\nCompleted 276.3 KiB/312.9 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 291.1 KiB/312.9 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/Yang2012-biopax2.owl to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/Yang2012-biopax2.owl\nCompleted 291.1 KiB/312.9 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 312.9 KiB/312.9 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/Yang2012-biopax3.owl to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/contents/Yang2012-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.4 KiB/7.4 KiB (113.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f174ee26f4323c9003a0/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Yang2012.sedml\ncreating dataset /Yang2012.sedml/autogen_report_for_task1, shape: (47, 631), type: float64\ndataset created, uuid: d-789744e4-a7eb0e7f-a09b-ef34a0-887cd6, chunk_size: (47, 631)\ncreating dataset /Yang2012.sedml/plot_1_task1, shape: (6, 631), type: float64\ndataset created, uuid: d-789744e4-a7eb0e7f-bfe3-980e65-06bdeb, chunk_size: (6, 631)\ncreating attribute combineArchiveLocation in /Yang2012.sedml\ncreating attribute uri in /Yang2012.sedml\ncreating attribute _type in /Yang2012.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Yang2012.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Yang2012.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Yang2012.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Yang2012.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Yang2012.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Yang2012.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Yang2012.sedml/autogen_report_for_task1\ncreating attribute uri in /Yang2012.sedml/autogen_report_for_task1\ncreating attribute _type in /Yang2012.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Yang2012.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Yang2012.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Yang2012.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Yang2012.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Yang2012.sedml/plot_1_task1\ncreating attribute sedmlId in /Yang2012.sedml/plot_1_task1\ncreating attribute sedmlName in /Yang2012.sedml/plot_1_task1\ncreating attribute uri in /Yang2012.sedml/plot_1_task1\ncreate_links: /\ngot link: Yang2012.sedml\ncreate_links: /Yang2012.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Yang2012.sedml/autogen_report_for_task1 to tgt: /Yang2012.sedml/autogen_report_for_task1, shape: (47, 631), type: float64\niterating over chunks for /Yang2012.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 47, 1), slice(0, 631, 1))\ndone with dataload for /Yang2012.sedml/autogen_report_for_task1\nwrite_dataset src: /Yang2012.sedml/plot_1_task1 to tgt: /Yang2012.sedml/plot_1_task1, shape: (6, 631), type: float64\niterating over chunks for /Yang2012.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 631, 1))\ndone with dataload for /Yang2012.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f174ee26f4323c9003a0\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 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.\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":1.556497,"sedDocuments":[{"location":"Yang2012.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  Yang2012.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 47 data sets\r\n    Plots (1):\r\n      plot_1_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: Yang2012.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":1.069532,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.249761,"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":0.40739,"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":"p1_curve_5_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.245813,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_A_plot","status":"SUCCEEDED"},{"id":"autogen_task1_C_plot","status":"SUCCEEDED"},{"id":"autogen_task1_E_plot","status":"SUCCEEDED"},{"id":"autogen_task1_P_plot","status":"SUCCEEDED"},{"id":"autogen_task1_T_plot","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_a1","status":"SUCCEEDED"},{"id":"autogen_task1_a2","status":"SUCCEEDED"},{"id":"autogen_task1_a3","status":"SUCCEEDED"},{"id":"autogen_task1_e","status":"SUCCEEDED"},{"id":"autogen_task1_u1","status":"SUCCEEDED"},{"id":"autogen_task1_u2","status":"SUCCEEDED"},{"id":"autogen_task1_u3","status":"SUCCEEDED"},{"id":"autogen_task1_u4","status":"SUCCEEDED"},{"id":"autogen_task1_u5","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_y","status":"SUCCEEDED"},{"id":"autogen_task1_b1","status":"SUCCEEDED"},{"id":"autogen_task1_b2","status":"SUCCEEDED"},{"id":"autogen_task1_c1","status":"SUCCEEDED"},{"id":"autogen_task1_c2","status":"SUCCEEDED"},{"id":"autogen_task1_c3","status":"SUCCEEDED"},{"id":"autogen_task1_c4","status":"SUCCEEDED"},{"id":"autogen_task1_c5","status":"SUCCEEDED"},{"id":"autogen_task1_tme","status":"SUCCEEDED"},{"id":"autogen_task1_normal_cell_growth","status":"SUCCEEDED"},{"id":"autogen_task1_normal_cell_death","status":"SUCCEEDED"},{"id":"autogen_task1_normal_cell_depletion","status":"SUCCEEDED"},{"id":"autogen_task1_endothelial_growth","status":"SUCCEEDED"},{"id":"autogen_task1_endothelial_death","status":"SUCCEEDED"},{"id":"autogen_task1_pre_angiogenesis","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_growth","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_death","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_depletion","status":"SUCCEEDED"},{"id":"autogen_task1_pa_death","status":"SUCCEEDED"},{"id":"autogen_task1_pa_conversion","status":"SUCCEEDED"},{"id":"autogen_task1_angiogenesis","status":"SUCCEEDED"},{"id":"autogen_task1_angiogenesis_cell_death","status":"SUCCEEDED"}]}]}]}