{"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    458      0 --:--:-- --:--:-- --:--:--   458\n\r100  253k  100  253k    0     0   578k      0 --:--:-- --:--:-- --:--:--  578k\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 (27.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/rawLog.txt\nCompleted 5.0 KiB/5.0 KiB (67.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/BIOMD0000000185_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000185_url.sedml/autogen_plot_for_task1.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 9%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/293.0 KiB (5.4 MiB/s) with 1 file(s) remaining\rCompleted 293.0 KiB/293.0 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/outputs/reports.h5\nCompleted 256.0 KiB/299.3 KiB (5.9 MiB/s) with 4 file(s) remaining\rCompleted 276.5 KiB/299.3 KiB (2.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/output.zip\nCompleted 276.5 KiB/299.3 KiB (2.9 MiB/s) with 3 file(s) remaining\rCompleted 285.1 KiB/299.3 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/outputs/plots.zip\nCompleted 285.1 KiB/299.3 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 287.8 KiB/299.3 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/rawLog.txt\nCompleted 287.8 KiB/299.3 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 299.3 KiB/299.3 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000185_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/outputs/BIOMD0000000185_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/BIOMD0000000185-biopax2.owl  \n  inflating: contents/BIOMD0000000185-biopax3.owl  \n  inflating: contents/BIOMD0000000185-matlab.m  \n  inflating: contents/BIOMD0000000185-octave.m  \n  inflating: contents/BIOMD0000000185.m  \n  inflating: contents/BIOMD0000000185.ode  \n  inflating: contents/BIOMD0000000185.pdf  \n  inflating: contents/BIOMD0000000185.png  \n  inflating: contents/BIOMD0000000185.svg  \n  inflating: contents/BIOMD0000000185.vcml  \n  inflating: contents/BIOMD0000000185_url.sedml  \n  inflating: contents/BIOMD0000000185_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 19.3 KiB/518.1 KiB (250.4 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000185-biopax2.owl to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185-biopax2.owl\nCompleted 19.3 KiB/518.1 KiB (250.4 KiB/s) with 15 file(s) remaining\rCompleted 26.6 KiB/518.1 KiB (214.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000185-matlab.m to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185-matlab.m\nCompleted 26.6 KiB/518.1 KiB (214.4 KiB/s) with 14 file(s) remaining\rCompleted 55.2 KiB/518.1 KiB (374.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000185-biopax3.owl to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185-biopax3.owl\nCompleted 55.2 KiB/518.1 KiB (374.5 KiB/s) with 13 file(s) remaining\rCompleted 62.5 KiB/518.1 KiB (418.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000185-octave.m to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185-octave.m\nCompleted 62.5 KiB/518.1 KiB (418.2 KiB/s) with 12 file(s) remaining\rCompleted 62.6 KiB/518.1 KiB (398.7 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/curation_notes.txt\nCompleted 62.6 KiB/518.1 KiB (398.7 KiB/s) with 11 file(s) remaining\rCompleted 87.9 KiB/518.1 KiB (552.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000185_url.sedml to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185_url.sedml\nCompleted 87.9 KiB/518.1 KiB (552.0 KiB/s) with 10 file(s) remaining\rCompleted 133.4 KiB/518.1 KiB (791.4 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000185.vcml to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185.vcml\nCompleted 133.4 KiB/518.1 KiB (791.4 KiB/s) with 9 file(s) remaining\rCompleted 136.0 KiB/518.1 KiB (749.4 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/metadata.rdf\nCompleted 136.0 KiB/518.1 KiB (749.4 KiB/s) with 8 file(s) remaining\rCompleted 170.9 KiB/518.1 KiB (930.2 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000185_url.xml to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185_url.xml\nCompleted 170.9 KiB/518.1 KiB (930.2 KiB/s) with 7 file(s) remaining\rCompleted 190.2 KiB/518.1 KiB (1.0 MiB/s) with 7 file(s) remaining  \rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/curation_image.jpeg\nCompleted 190.2 KiB/518.1 KiB (1.0 MiB/s) with 6 file(s) remaining\rCompleted 226.1 KiB/518.1 KiB (1.2 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000185.svg to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185.svg\nCompleted 226.1 KiB/518.1 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 233.4 KiB/518.1 KiB (1.0 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000185.m to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185.m\nCompleted 233.4 KiB/518.1 KiB (1.0 MiB/s) with 4 file(s) remaining\rCompleted 237.9 KiB/518.1 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000185.ode to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185.ode\nCompleted 237.9 KiB/518.1 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 239.8 KiB/518.1 KiB (1.0 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/manifest.xml\nCompleted 239.8 KiB/518.1 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 430.9 KiB/518.1 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000185.pdf to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185.pdf\nCompleted 430.9 KiB/518.1 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 518.1 KiB/518.1 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000185.png to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/contents/BIOMD0000000185.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (127.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471095549c0d898ffddd3d3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000185_url.sedml\ncreating dataset /BIOMD0000000185_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-92f2dd16-687eaa93-504e-fc0faf-a4e469, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000185_url.sedml/autogen_report_for_task1, shape: (49, 1001), type: float64\ndataset created, uuid: d-92f2dd16-687eaa93-c2cd-399c27-362af3, chunk_size: (49, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000185_url.sedml\ncreating attribute uri in /BIOMD0000000185_url.sedml\ncreating attribute _type in /BIOMD0000000185_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000185_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000185_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000185_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000185_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000185_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000185_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000185_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000185_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000185_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000185_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000185_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000185_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000185_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000185_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000185_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000185_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000185_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000185_url.sedml\ncreate_links: /BIOMD0000000185_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000185_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000185_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000185_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000185_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000185_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000185_url.sedml/autogen_report_for_task1, shape: (49, 1001), type: float64\niterating over chunks for /BIOMD0000000185_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 49, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000185_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471095549c0d898ffddd3d3\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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.87905,"sedDocuments":[{"location":"BIOMD0000000185_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  BIOMD0000000185_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 49 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000185_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":1.360249,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.271214,"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":0.380833,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_X1","status":"SUCCEEDED"},{"id":"autogen_task1_Y1","status":"SUCCEEDED"},{"id":"autogen_task1_Z1","status":"SUCCEEDED"},{"id":"autogen_task1_V1","status":"SUCCEEDED"},{"id":"autogen_task1_X2","status":"SUCCEEDED"},{"id":"autogen_task1_Y2","status":"SUCCEEDED"},{"id":"autogen_task1_Z2","status":"SUCCEEDED"},{"id":"autogen_task1_V2","status":"SUCCEEDED"},{"id":"autogen_task1_F","status":"SUCCEEDED"},{"id":"autogen_task1_v_1","status":"SUCCEEDED"},{"id":"autogen_task1_K1","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_v_2","status":"SUCCEEDED"},{"id":"autogen_task1_K2","status":"SUCCEEDED"},{"id":"autogen_task1_vc","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_Kc","status":"SUCCEEDED"},{"id":"autogen_task1_L","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_v_4","status":"SUCCEEDED"},{"id":"autogen_task1_K4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_v_6","status":"SUCCEEDED"},{"id":"autogen_task1_K6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_v_8","status":"SUCCEEDED"},{"id":"autogen_task1_K8","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"},{"id":"autogen_task1_R5","status":"SUCCEEDED"},{"id":"autogen_task1_R6","status":"SUCCEEDED"},{"id":"autogen_task1_R7","status":"SUCCEEDED"},{"id":"autogen_task1_R8","status":"SUCCEEDED"},{"id":"autogen_task1_R9","status":"SUCCEEDED"},{"id":"autogen_task1_R10","status":"SUCCEEDED"},{"id":"autogen_task1_R11","status":"SUCCEEDED"},{"id":"autogen_task1_R12","status":"SUCCEEDED"},{"id":"autogen_task1_R13","status":"SUCCEEDED"},{"id":"autogen_task1_R14","status":"SUCCEEDED"},{"id":"autogen_task1_R15","status":"SUCCEEDED"},{"id":"autogen_task1_R16","status":"SUCCEEDED"},{"id":"autogen_task1_R17","status":"SUCCEEDED"},{"id":"autogen_task1_R18","status":"SUCCEEDED"},{"id":"autogen_task1_R19","status":"SUCCEEDED"},{"id":"autogen_task1_R20","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.539246,"curves":[{"id":"autogen_curve_task1_X1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Y1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_V1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Y2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_V2","status":"SUCCEEDED"}]}]}]}