{"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    405      0 --:--:-- --:--:-- --:--:--   406\n\r100  286k  100  286k    0     0   618k      0 --:--:-- --:--:-- --:--:--  618k\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 (25.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/rawLog.txt\nCompleted 4.0 KiB/4.0 KiB (50.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/BIOMD0000000539.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000539.sedml/plot_1_task1.pdf (deflated 23%)\n  adding: outputs/reports.h5 (deflated 13%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 197.3 KiB/197.3 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/outputs/reports.h5\nCompleted 186.7 KiB/217.1 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/output.zip\nCompleted 186.7 KiB/217.1 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 198.6 KiB/217.1 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/outputs/plots.zip\nCompleted 198.6 KiB/217.1 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 201.2 KiB/217.1 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/rawLog.txt\nCompleted 201.2 KiB/217.1 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 217.1 KiB/217.1 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000539.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/outputs/BIOMD0000000539.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000539-biopax2.owl  \n  inflating: contents/BIOMD0000000539-biopax3.owl  \n  inflating: contents/BIOMD0000000539-matlab.m  \n  inflating: contents/BIOMD0000000539-octave.m  \n  inflating: contents/BIOMD0000000539.cps  \n  inflating: contents/BIOMD0000000539.m  \n  inflating: contents/BIOMD0000000539.ode  \n  inflating: contents/BIOMD0000000539.pdf  \n  inflating: contents/BIOMD0000000539.png  \n  inflating: contents/BIOMD0000000539.sci  \n  inflating: contents/BIOMD0000000539.sedml  \n  inflating: contents/BIOMD0000000539.svg  \n  inflating: contents/BIOMD0000000539.vcml  \n  inflating: contents/BIOMD0000000539_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 24.0 KiB/576.2 KiB (313.4 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000539-biopax3.owl to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539-biopax3.owl\nCompleted 24.0 KiB/576.2 KiB (313.4 KiB/s) with 17 file(s) remaining\rCompleted 29.4 KiB/576.2 KiB (282.0 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000539-matlab.m to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539-matlab.m\nCompleted 29.4 KiB/576.2 KiB (282.0 KiB/s) with 16 file(s) remaining\rCompleted 45.9 KiB/576.2 KiB (371.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000539-biopax2.owl to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539-biopax2.owl\nCompleted 45.9 KiB/576.2 KiB (371.2 KiB/s) with 15 file(s) remaining\rCompleted 51.3 KiB/576.2 KiB (401.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000539-octave.m to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539-octave.m\nCompleted 51.3 KiB/576.2 KiB (401.4 KiB/s) with 14 file(s) remaining\rCompleted 89.3 KiB/576.2 KiB (647.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000539_url.xml to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539_url.xml\nCompleted 89.3 KiB/576.2 KiB (647.0 KiB/s) with 13 file(s) remaining\rCompleted 170.7 KiB/576.2 KiB (1.2 MiB/s) with 13 file(s) remaining \rupload: contents/BIOMD0000000539.png to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539.png\nCompleted 170.7 KiB/576.2 KiB (1.2 MiB/s) with 12 file(s) remaining\rCompleted 171.1 KiB/576.2 KiB (1.1 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000539.sci to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539.sci\nCompleted 171.1 KiB/576.2 KiB (1.1 MiB/s) with 11 file(s) remaining\rCompleted 199.2 KiB/576.2 KiB (1.2 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000539.svg to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539.svg\nCompleted 199.2 KiB/576.2 KiB (1.2 MiB/s) with 10 file(s) remaining\rCompleted 217.1 KiB/576.2 KiB (1.3 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000539.sedml to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539.sedml\nCompleted 217.1 KiB/576.2 KiB (1.3 MiB/s) with 9 file(s) remaining\rCompleted 217.2 KiB/576.2 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/curation_notes.txt\nCompleted 217.2 KiB/576.2 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 218.3 KiB/576.2 KiB (1.1 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/metadata.rdf\nCompleted 218.3 KiB/576.2 KiB (1.1 MiB/s) with 7 file(s) remaining\rCompleted 220.4 KiB/576.2 KiB (1.1 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/manifest.xml\nCompleted 220.4 KiB/576.2 KiB (1.1 MiB/s) with 6 file(s) remaining\rCompleted 223.8 KiB/576.2 KiB (1.1 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000539.ode to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539.ode\nCompleted 223.8 KiB/576.2 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 395.8 KiB/576.2 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000539.pdf to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539.pdf\nCompleted 395.8 KiB/576.2 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 448.6 KiB/576.2 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000539.vcml to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539.vcml\nCompleted 448.6 KiB/576.2 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 511.4 KiB/576.2 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/curation_image.png\nCompleted 511.4 KiB/576.2 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 570.7 KiB/576.2 KiB (2.5 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000539.cps to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539.cps\nCompleted 570.7 KiB/576.2 KiB (2.5 MiB/s) with 1 file(s) remaining\rCompleted 576.2 KiB/576.2 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000539.m to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/contents/BIOMD0000000539.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.3 KiB/9.3 KiB (137.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647111459a62a8be53f89213/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000539.sedml\ncreating dataset /BIOMD0000000539.sedml/autogen_report_for_task1, shape: (30, 1001), type: float64\ndataset created, uuid: d-3c4d94a7-943407d6-f89f-098530-3c4836, chunk_size: (30, 1001)\ncreating dataset /BIOMD0000000539.sedml/plot_1_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-3c4d94a7-943407d6-1c67-fdd263-23070e, chunk_size: (7, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000539.sedml\ncreating attribute uri in /BIOMD0000000539.sedml\ncreating attribute _type in /BIOMD0000000539.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000539.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000539.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000539.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000539.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000539.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000539.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000539.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000539.sedml/autogen_report_for_task1\ncreating attribute _type in /BIOMD0000000539.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000539.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000539.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000539.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000539.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000539.sedml/plot_1_task1\ncreating attribute sedmlId in /BIOMD0000000539.sedml/plot_1_task1\ncreating attribute sedmlName in /BIOMD0000000539.sedml/plot_1_task1\ncreating attribute uri in /BIOMD0000000539.sedml/plot_1_task1\ncreate_links: /\ngot link: BIOMD0000000539.sedml\ncreate_links: /BIOMD0000000539.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /BIOMD0000000539.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000539.sedml/autogen_report_for_task1, shape: (30, 1001), type: float64\niterating over chunks for /BIOMD0000000539.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 30, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000539.sedml/autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000539.sedml/plot_1_task1 to tgt: /BIOMD0000000539.sedml/plot_1_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000539.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000539.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647111459a62a8be53f89213\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.\nProcess 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.592084,"sedDocuments":[{"location":"BIOMD0000000539.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  BIOMD0000000539.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 30 data sets\r\n    Plots (1):\r\n      plot_1_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000539.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":1.102668,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.238758,"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":0.489353,"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":"p1_curve_6_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.241776,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_AgB","status":"SUCCEEDED"},{"id":"autogen_task1_gB","status":"SUCCEEDED"},{"id":"autogen_task1_rB","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_AB","status":"SUCCEEDED"},{"id":"autogen_task1_theta","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_rhob","status":"SUCCEEDED"},{"id":"autogen_task1_rhof","status":"SUCCEEDED"},{"id":"autogen_task1_deltar","status":"SUCCEEDED"},{"id":"autogen_task1_rhoA","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_deltaA","status":"SUCCEEDED"},{"id":"autogen_task1_deltaB","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_deltaAB","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_A_binds_gB","status":"SUCCEEDED"},{"id":"autogen_task1_gB_releases_A","status":"SUCCEEDED"},{"id":"autogen_task1_basal_transcription_B","status":"SUCCEEDED"},{"id":"autogen_task1_stim_transcription_B","status":"SUCCEEDED"},{"id":"autogen_task1_degradation_mRNA_B","status":"SUCCEEDED"},{"id":"autogen_task1_production_A","status":"SUCCEEDED"},{"id":"autogen_task1_degradation_A","status":"SUCCEEDED"},{"id":"autogen_task1_translation_B","status":"SUCCEEDED"},{"id":"autogen_task1_degradation_B","status":"SUCCEEDED"},{"id":"autogen_task1_formation_dimer","status":"SUCCEEDED"},{"id":"autogen_task1_degradation_dimer","status":"SUCCEEDED"}]}]}]}