{"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    457      0 --:--:-- --:--:-- --:--:--   458\n\r100  323k  100  323k    0     0   764k      0 --:--:-- --:--:-- --:--:--  764k\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 (25.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (58.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/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/BIOMD0000000351_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000351_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 17%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 164.0 KiB/164.0 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/outputs/reports.h5\nCompleted 146.2 KiB/167.5 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/output.zip\nCompleted 146.2 KiB/167.5 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 148.8 KiB/167.5 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/rawLog.txt\nCompleted 148.8 KiB/167.5 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 156.4 KiB/167.5 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/outputs/plots.zip\nCompleted 156.4 KiB/167.5 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 167.5 KiB/167.5 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000351_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/outputs/BIOMD0000000351_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000351-biopax2.owl  \n  inflating: contents/BIOMD0000000351-biopax3.owl  \n  inflating: contents/BIOMD0000000351-matlab.m  \n  inflating: contents/BIOMD0000000351-octave.m  \n  inflating: contents/BIOMD0000000351.m  \n  inflating: contents/BIOMD0000000351.ode  \n  inflating: contents/BIOMD0000000351.pdf  \n  inflating: contents/BIOMD0000000351.png  \n  inflating: contents/BIOMD0000000351.svg  \n  inflating: contents/BIOMD0000000351.vcml  \n  inflating: contents/BIOMD0000000351_url.sedml  \n  inflating: contents/BIOMD0000000351_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 17.2 KiB/559.0 KiB (184.1 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000351-biopax2.owl to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351-biopax2.owl\nCompleted 17.2 KiB/559.0 KiB (184.1 KiB/s) with 15 file(s) remaining\rCompleted 23.8 KiB/559.0 KiB (233.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000351-octave.m to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351-octave.m\nCompleted 23.8 KiB/559.0 KiB (233.0 KiB/s) with 14 file(s) remaining\rCompleted 30.4 KiB/559.0 KiB (268.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000351-matlab.m to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351-matlab.m\nCompleted 30.4 KiB/559.0 KiB (268.2 KiB/s) with 13 file(s) remaining\rCompleted 114.4 KiB/559.0 KiB (902.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000351.png to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351.png\nCompleted 114.4 KiB/559.0 KiB (902.8 KiB/s) with 12 file(s) remaining\rCompleted 142.0 KiB/559.0 KiB (1019.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000351.svg to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351.svg\nCompleted 142.0 KiB/559.0 KiB (1019.8 KiB/s) with 11 file(s) remaining\rCompleted 180.8 KiB/559.0 KiB (1.2 MiB/s) with 11 file(s) remaining   \rupload: contents/BIOMD0000000351.vcml to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351.vcml\nCompleted 180.8 KiB/559.0 KiB (1.2 MiB/s) with 10 file(s) remaining\rCompleted 212.8 KiB/559.0 KiB (1.4 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000351_url.xml to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351_url.xml\nCompleted 212.8 KiB/559.0 KiB (1.4 MiB/s) with 9 file(s) remaining\rCompleted 213.2 KiB/559.0 KiB (1.3 MiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/curation_notes.txt\nCompleted 213.2 KiB/559.0 KiB (1.3 MiB/s) with 8 file(s) remaining\rCompleted 236.4 KiB/559.0 KiB (1.4 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000351_url.sedml to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351_url.sedml\nCompleted 236.4 KiB/559.0 KiB (1.4 MiB/s) with 7 file(s) remaining\rCompleted 238.3 KiB/559.0 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/manifest.xml\nCompleted 238.3 KiB/559.0 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 263.9 KiB/559.0 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000351-biopax3.owl to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351-biopax3.owl\nCompleted 263.9 KiB/559.0 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 349.4 KiB/559.0 KiB (1.7 MiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/curation_image.png\nCompleted 349.4 KiB/559.0 KiB (1.7 MiB/s) with 4 file(s) remaining\rCompleted 354.2 KiB/559.0 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/metadata.rdf\nCompleted 354.2 KiB/559.0 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 547.9 KiB/559.0 KiB (2.6 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000351.pdf to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351.pdf\nCompleted 547.9 KiB/559.0 KiB (2.6 MiB/s) with 2 file(s) remaining\rCompleted 554.5 KiB/559.0 KiB (2.6 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000351.m to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351.m\nCompleted 554.5 KiB/559.0 KiB (2.6 MiB/s) with 1 file(s) remaining\rCompleted 559.0 KiB/559.0 KiB (2.6 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000351.ode to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/contents/BIOMD0000000351.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (143.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b899a62a8be53f7bcb8/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000351_url.sedml\ncreating dataset /BIOMD0000000351_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-80a5219b-f19e109d-67bb-6491cf-01a7c8, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000351_url.sedml/autogen_report_for_task1, shape: (43, 1001), type: float64\ndataset created, uuid: d-80a5219b-f19e109d-7e23-32fd71-2edc95, chunk_size: (43, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000351_url.sedml\ncreating attribute uri in /BIOMD0000000351_url.sedml\ncreating attribute _type in /BIOMD0000000351_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000351_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000351_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000351_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000351_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000351_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000351_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000351_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000351_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000351_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000351_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000351_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000351_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000351_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000351_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000351_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000351_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000351_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000351_url.sedml\ncreate_links: /BIOMD0000000351_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000351_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000351_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000351_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000351_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000351_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000351_url.sedml/autogen_report_for_task1, shape: (43, 1001), type: float64\niterating over chunks for /BIOMD0000000351_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 43, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000351_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710b899a62a8be53f7bcb8\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.\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.\nProcess and upload the outputs of the simulation run ... 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":1.294123,"sedDocuments":[{"location":"BIOMD0000000351_url.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  BIOMD0000000351_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 43 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000351_url.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_plot_for_task1`\r\n      `autogen_report_for_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: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_plot_for_task1` ...","duration":0.917894,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.154017,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.289454,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_D_II","status":"SUCCEEDED"},{"id":"autogen_task1_D_IA","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_aux","status":"SUCCEEDED"},{"id":"autogen_task1_pi_I","status":"SUCCEEDED"},{"id":"autogen_task1_d_r","status":"SUCCEEDED"},{"id":"autogen_task1_d_A","status":"SUCCEEDED"},{"id":"autogen_task1_d_II","status":"SUCCEEDED"},{"id":"autogen_task1_d_IA","status":"SUCCEEDED"},{"id":"autogen_task1_k_II","status":"SUCCEEDED"},{"id":"autogen_task1_k_IA","status":"SUCCEEDED"},{"id":"autogen_task1_B_d","status":"SUCCEEDED"},{"id":"autogen_task1_f_A","status":"SUCCEEDED"},{"id":"autogen_task1_gamma_I","status":"SUCCEEDED"},{"id":"autogen_task1_K_aux","status":"SUCCEEDED"},{"id":"autogen_task1_K_II","status":"SUCCEEDED"},{"id":"autogen_task1_K_IA","status":"SUCCEEDED"},{"id":"autogen_task1_f_c","status":"SUCCEEDED"},{"id":"autogen_task1_w_A","status":"SUCCEEDED"},{"id":"autogen_task1_w_I","status":"SUCCEEDED"},{"id":"autogen_task1_w_D","status":"SUCCEEDED"},{"id":"autogen_task1_d_I","status":"SUCCEEDED"},{"id":"autogen_task1_pi_A","status":"SUCCEEDED"},{"id":"autogen_task1_k_Am","status":"SUCCEEDED"},{"id":"autogen_task1_kprime_IA","status":"SUCCEEDED"},{"id":"autogen_task1_kprime_II","status":"SUCCEEDED"},{"id":"autogen_task1_aux_basal","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_0000001","status":"SUCCEEDED"},{"id":"autogen_task1_reac_DIA","status":"SUCCEEDED"},{"id":"autogen_task1_reac_DII","status":"SUCCEEDED"},{"id":"autogen_task1_reac_degrI","status":"SUCCEEDED"},{"id":"autogen_task1_reac_degrA","status":"SUCCEEDED"},{"id":"autogen_task1_reac_degrDIA","status":"SUCCEEDED"},{"id":"autogen_task1_reac_degrDII","status":"SUCCEEDED"},{"id":"autogen_task1_reac_DIAxA","status":"SUCCEEDED"},{"id":"autogen_task1_reac_DIIxI","status":"SUCCEEDED"},{"id":"autogen_task1_reac_degrR","status":"SUCCEEDED"},{"id":"autogen_task1_reac_prodI","status":"SUCCEEDED"},{"id":"autogen_task1_reac_prodA","status":"SUCCEEDED"},{"id":"autogen_task1_reac_prodR","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.346704,"curves":[{"id":"autogen_curve_task1_I","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_D_II","status":"SUCCEEDED"},{"id":"autogen_curve_task1_D_IA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_aux","status":"SUCCEEDED"}]}]}]}