{"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    423      0 --:--:-- --:--:-- --:--:--   423\n\r100  516k  100  516k    0     0  1131k      0 --:--:-- --:--:-- --:--:-- 1131k\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 (26.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/rawLog.txt\nCompleted 6.0 KiB/6.0 KiB (84.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/BIOMD0000000586_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000586_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/279.9 KiB (6.7 MiB/s) with 1 file(s) remaining\rCompleted 279.9 KiB/279.9 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/outputs/reports.h5\nCompleted 256.0 KiB/278.7 KiB (5.5 MiB/s) with 4 file(s) remaining\rCompleted 258.7 KiB/278.7 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/rawLog.txt\nCompleted 258.7 KiB/278.7 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 260.2 KiB/278.7 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/output.zip\nCompleted 260.2 KiB/278.7 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 271.0 KiB/278.7 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000586_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/outputs/BIOMD0000000586_url.sedml/autogen_plot_for_task1.pdf\nCompleted 271.0 KiB/278.7 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 278.7 KiB/278.7 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000586-biopax2.owl  \n  inflating: contents/BIOMD0000000586-biopax3.owl  \n  inflating: contents/BIOMD0000000586-matlab.m  \n  inflating: contents/BIOMD0000000586-octave.m  \n  inflating: contents/BIOMD0000000586.m  \n  inflating: contents/BIOMD0000000586.ode  \n  inflating: contents/BIOMD0000000586.pdf  \n  inflating: contents/BIOMD0000000586.png  \n  inflating: contents/BIOMD0000000586.svg  \n  inflating: contents/BIOMD0000000586_url.sedml  \n  inflating: contents/BIOMD0000000586_url.xml  \n  inflating: contents/BMD586-7_annotations.pdf  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 50.6 KiB/913.2 KiB (621.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000586-biopax3.owl to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586-biopax3.owl\nCompleted 50.6 KiB/913.2 KiB (621.5 KiB/s) with 15 file(s) remaining\rCompleted 60.5 KiB/913.2 KiB (493.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000586-octave.m to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586-octave.m\nCompleted 60.5 KiB/913.2 KiB (493.6 KiB/s) with 14 file(s) remaining\rCompleted 90.2 KiB/913.2 KiB (705.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000586-biopax2.owl to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586-biopax2.owl\nCompleted 90.2 KiB/913.2 KiB (705.1 KiB/s) with 13 file(s) remaining\rCompleted 92.0 KiB/913.2 KiB (694.8 KiB/s) with 13 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/manifest.xml\nCompleted 92.0 KiB/913.2 KiB (694.8 KiB/s) with 12 file(s) remaining\rCompleted 101.9 KiB/913.2 KiB (742.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000586-matlab.m to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586-matlab.m\nCompleted 101.9 KiB/913.2 KiB (742.7 KiB/s) with 11 file(s) remaining\rCompleted 357.9 KiB/913.2 KiB (2.3 MiB/s) with 11 file(s) remaining  \rCompleted 390.6 KiB/913.2 KiB (2.4 MiB/s) with 11 file(s) remaining  \rupload: contents/BIOMD0000000586_url.sedml to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586_url.sedml\nCompleted 390.6 KiB/913.2 KiB (2.4 MiB/s) with 10 file(s) remaining\rCompleted 646.6 KiB/913.2 KiB (3.9 MiB/s) with 10 file(s) remaining\rCompleted 717.0 KiB/913.2 KiB (4.2 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000586_url.xml to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586_url.xml\nCompleted 717.0 KiB/913.2 KiB (4.2 MiB/s) with 9 file(s) remaining\rCompleted 746.8 KiB/913.2 KiB (4.2 MiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/curation_image.png\nCompleted 746.8 KiB/913.2 KiB (4.2 MiB/s) with 8 file(s) remaining\rCompleted 811.1 KiB/913.2 KiB (4.4 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000586.svg to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586.svg\nCompleted 811.1 KiB/913.2 KiB (4.4 MiB/s) with 7 file(s) remaining\rCompleted 829.5 KiB/913.2 KiB (4.5 MiB/s) with 7 file(s) remaining\rupload: contents/BMD586-7_annotations.pdf to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BMD586-7_annotations.pdf\nCompleted 829.5 KiB/913.2 KiB (4.5 MiB/s) with 6 file(s) remaining\rCompleted 834.6 KiB/913.2 KiB (4.4 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/metadata.rdf\nCompleted 834.6 KiB/913.2 KiB (4.4 MiB/s) with 5 file(s) remaining\rCompleted 844.5 KiB/913.2 KiB (3.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000586.m to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586.m\nCompleted 844.5 KiB/913.2 KiB (3.8 MiB/s) with 4 file(s) remaining\rCompleted 845.0 KiB/913.2 KiB (3.6 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/curation_notes.txt\nCompleted 845.0 KiB/913.2 KiB (3.6 MiB/s) with 3 file(s) remaining\rCompleted 851.6 KiB/913.2 KiB (3.5 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000586.pdf to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586.pdf\nCompleted 851.6 KiB/913.2 KiB (3.5 MiB/s) with 2 file(s) remaining\rCompleted 906.1 KiB/913.2 KiB (3.6 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000586.png to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586.png\nCompleted 906.1 KiB/913.2 KiB (3.6 MiB/s) with 1 file(s) remaining\rCompleted 913.2 KiB/913.2 KiB (3.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000586.ode to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/contents/BIOMD0000000586.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (141.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f156da4ff2037f59bf28/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000586_url.sedml\ncreating dataset /BIOMD0000000586_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\ndataset created, uuid: d-b8528da4-1b3f847e-043c-0bae65-e96978, chunk_size: (11, 1001)\ncreating dataset /BIOMD0000000586_url.sedml/autogen_report_for_task1, shape: (60, 1001), type: float64\ndataset created, uuid: d-b8528da4-1b3f847e-93b1-c952d5-683940, chunk_size: (60, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000586_url.sedml\ncreating attribute uri in /BIOMD0000000586_url.sedml\ncreating attribute _type in /BIOMD0000000586_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000586_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000586_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000586_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000586_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000586_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000586_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000586_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000586_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000586_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000586_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000586_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000586_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000586_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000586_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000586_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000586_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000586_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000586_url.sedml\ncreate_links: /BIOMD0000000586_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000586_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000586_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\niterating over chunks for /BIOMD0000000586_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000586_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000586_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000586_url.sedml/autogen_report_for_task1, shape: (60, 1001), type: float64\niterating over chunks for /BIOMD0000000586_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 60, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000586_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f156da4ff2037f59bf28\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":2.094573,"sedDocuments":[{"location":"BIOMD0000000586_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  BIOMD0000000586_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 60 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 10 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000586_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":1.499004,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.281773,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.448827,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_G0","status":"SUCCEEDED"},{"id":"autogen_task1_G1","status":"SUCCEEDED"},{"id":"autogen_task1_rA","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_rI","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_AI","status":"SUCCEEDED"},{"id":"autogen_task1_A2","status":"SUCCEEDED"},{"id":"autogen_task1_G2","status":"SUCCEEDED"},{"id":"autogen_task1_G3","status":"SUCCEEDED"},{"id":"autogen_task1_Theta","status":"SUCCEEDED"},{"id":"autogen_task1_Alpha","status":"SUCCEEDED"},{"id":"autogen_task1_rho_f","status":"SUCCEEDED"},{"id":"autogen_task1_rho_b","status":"SUCCEEDED"},{"id":"autogen_task1_rho_0","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_delta_m","status":"SUCCEEDED"},{"id":"autogen_task1_delta_p","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_epsilon","status":"SUCCEEDED"},{"id":"autogen_task1_epsilon_1","status":"SUCCEEDED"},{"id":"autogen_task1_a_01","status":"SUCCEEDED"},{"id":"autogen_task1_a_12","status":"SUCCEEDED"},{"id":"autogen_task1_a_23","status":"SUCCEEDED"},{"id":"autogen_task1_t_10","status":"SUCCEEDED"},{"id":"autogen_task1_t_21","status":"SUCCEEDED"},{"id":"autogen_task1_t_32","status":"SUCCEEDED"},{"id":"autogen_task1__3sites","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_17","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_1","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_0","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_18","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_3","status":"SUCCEEDED"},{"id":"autogen_task1_ModelValue_2","status":"SUCCEEDED"},{"id":"autogen_task1_yeast","status":"SUCCEEDED"},{"id":"autogen_task1_G1____G0___A2","status":"SUCCEEDED"},{"id":"autogen_task1_G0___A2____G1","status":"SUCCEEDED"},{"id":"autogen_task1_G____G___rI","status":"SUCCEEDED"},{"id":"autogen_task1_G1____G1___rI","status":"SUCCEEDED"},{"id":"autogen_task1_rA___","status":"SUCCEEDED"},{"id":"autogen_task1_____rA","status":"SUCCEEDED"},{"id":"autogen_task1_rI___","status":"SUCCEEDED"},{"id":"autogen_task1_rA____rA___A","status":"SUCCEEDED"},{"id":"autogen_task1_I___","status":"SUCCEEDED"},{"id":"autogen_task1_rI____rI___I","status":"SUCCEEDED"},{"id":"autogen_task1_A___","status":"SUCCEEDED"},{"id":"autogen_task1_A___I____AI","status":"SUCCEEDED"},{"id":"autogen_task1__2___A____A2","status":"SUCCEEDED"},{"id":"autogen_task1_A2____2___A","status":"SUCCEEDED"},{"id":"autogen_task1_AI____A___I","status":"SUCCEEDED"},{"id":"autogen_task1_AI___","status":"SUCCEEDED"},{"id":"autogen_task1_A2___","status":"SUCCEEDED"},{"id":"autogen_task1_G1___A2____G2","status":"SUCCEEDED"},{"id":"autogen_task1_G2____G1___A2","status":"SUCCEEDED"},{"id":"autogen_task1_G2____G2___rI","status":"SUCCEEDED"},{"id":"autogen_task1_G2___A2____G3","status":"SUCCEEDED"},{"id":"autogen_task1_G3____G2___A2","status":"SUCCEEDED"},{"id":"autogen_task1_G3____G3___rI","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.571028,"curves":[{"id":"autogen_curve_task1_G0","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_rA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I","status":"SUCCEEDED"},{"id":"autogen_curve_task1_rI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G3","status":"SUCCEEDED"}]}]}]}