{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    431      0 --:--:-- --:--:-- --:--:--   431\n\r100  206k  100  206k    0     0   465k      0 --:--:-- --:--:-- --:--:--  465k\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 (25.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/rawLog.txt\nCompleted 5.1 KiB/5.1 KiB (69.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/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/BIOMD0000000126_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000126_url.sedml/autogen_plot_for_task1.pdf (deflated 25%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 253.7 KiB/253.7 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/outputs/reports.h5\nCompleted 238.4 KiB/262.2 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/output.zip\nCompleted 238.4 KiB/262.2 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 247.4 KiB/262.2 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/outputs/plots.zip\nCompleted 247.4 KiB/262.2 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 250.1 KiB/262.2 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/rawLog.txt\nCompleted 250.1 KiB/262.2 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 262.2 KiB/262.2 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000126_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/outputs/BIOMD0000000126_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/BIOMD0000000126-biopax2.owl  \n  inflating: contents/BIOMD0000000126-biopax3.owl  \n  inflating: contents/BIOMD0000000126-matlab.m  \n  inflating: contents/BIOMD0000000126-octave.m  \n  inflating: contents/BIOMD0000000126.m  \n  inflating: contents/BIOMD0000000126.ode  \n  inflating: contents/BIOMD0000000126.pdf  \n  inflating: contents/BIOMD0000000126.png  \n  inflating: contents/BIOMD0000000126.svg  \n  inflating: contents/BIOMD0000000126.vcml  \n  inflating: contents/BIOMD0000000126_url.sedml  \n  inflating: contents/BIOMD0000000126_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 20.5 KiB/~458.2 KiB (325.1 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000126-biopax2.owl to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126-biopax2.owl\nCompleted 20.5 KiB/~458.2 KiB (325.1 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 28.8 KiB/465.4 KiB (260.2 KiB/s) with 15 file(s) remaining                   \rupload: contents/BIOMD0000000126-matlab.m to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126-matlab.m\nCompleted 28.8 KiB/465.4 KiB (260.2 KiB/s) with 14 file(s) remaining\rCompleted 37.2 KiB/465.4 KiB (317.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000126-octave.m to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126-octave.m\nCompleted 37.2 KiB/465.4 KiB (317.1 KiB/s) with 13 file(s) remaining\rCompleted 40.3 KiB/465.4 KiB (317.0 KiB/s) with 13 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/curation_image.png\nCompleted 40.3 KiB/465.4 KiB (317.0 KiB/s) with 12 file(s) remaining\rCompleted 67.5 KiB/465.4 KiB (477.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000126.svg to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126.svg\nCompleted 67.5 KiB/465.4 KiB (477.9 KiB/s) with 11 file(s) remaining\rCompleted 106.5 KiB/465.4 KiB (690.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000126.png to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126.png\nCompleted 106.5 KiB/465.4 KiB (690.8 KiB/s) with 10 file(s) remaining\rCompleted 131.6 KiB/465.4 KiB (810.5 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000126_url.sedml to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126_url.sedml\nCompleted 131.6 KiB/465.4 KiB (810.5 KiB/s) with 9 file(s) remaining\rCompleted 136.9 KiB/465.4 KiB (808.0 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/metadata.rdf\nCompleted 136.9 KiB/465.4 KiB (808.0 KiB/s) with 8 file(s) remaining\rCompleted 145.3 KiB/465.4 KiB (800.7 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000126.m to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126.m\nCompleted 145.3 KiB/465.4 KiB (800.7 KiB/s) with 7 file(s) remaining\rCompleted 175.3 KiB/465.4 KiB (955.8 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000126-biopax3.owl to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126-biopax3.owl\nCompleted 175.3 KiB/465.4 KiB (955.8 KiB/s) with 6 file(s) remaining\rCompleted 175.4 KiB/465.4 KiB (941.9 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/curation_notes.txt\nCompleted 175.4 KiB/465.4 KiB (941.9 KiB/s) with 5 file(s) remaining\rCompleted 215.9 KiB/465.4 KiB (1.1 MiB/s) with 5 file(s) remaining  \rupload: contents/BIOMD0000000126_url.xml to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126_url.xml\nCompleted 215.9 KiB/465.4 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 221.6 KiB/465.4 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000126.ode to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126.ode\nCompleted 221.6 KiB/465.4 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 420.5 KiB/465.4 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000126.pdf to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126.pdf\nCompleted 420.5 KiB/465.4 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 422.3 KiB/465.4 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/manifest.xml\nCompleted 422.3 KiB/465.4 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 465.4 KiB/465.4 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000126.vcml to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/contents/BIOMD0000000126.vcml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (129.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108959a62a8be53f76361/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000126_url.sedml\ncreating dataset /BIOMD0000000126_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-3c423342-b7d761b0-33cb-3f5cc1-0e189c, chunk_size: (10, 1001)\ncreating dataset /BIOMD0000000126_url.sedml/autogen_report_for_task1, shape: (46, 1001), type: float64\ndataset created, uuid: d-3c423342-b7d761b0-bfd2-145c27-b61a28, chunk_size: (46, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000126_url.sedml\ncreating attribute uri in /BIOMD0000000126_url.sedml\ncreating attribute _type in /BIOMD0000000126_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000126_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000126_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000126_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000126_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000126_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000126_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000126_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000126_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000126_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000126_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000126_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000126_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000126_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000126_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000126_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000126_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000126_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000126_url.sedml\ncreate_links: /BIOMD0000000126_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000126_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000126_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000126_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000126_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000126_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000126_url.sedml/autogen_report_for_task1, shape: (46, 1001), type: float64\niterating over chunks for /BIOMD0000000126_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 46, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000126_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647108959a62a8be53f76361\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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.\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":1.868273,"sedDocuments":[{"location":"BIOMD0000000126_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  BIOMD0000000126_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 46 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 9 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000126_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":1.363321,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.292676,"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":0.359547,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_C1","status":"SUCCEEDED"},{"id":"autogen_task1_C2","status":"SUCCEEDED"},{"id":"autogen_task1_C3","status":"SUCCEEDED"},{"id":"autogen_task1_IC3","status":"SUCCEEDED"},{"id":"autogen_task1_IC2","status":"SUCCEEDED"},{"id":"autogen_task1_IM1","status":"SUCCEEDED"},{"id":"autogen_task1_IM2","status":"SUCCEEDED"},{"id":"autogen_task1_O","status":"SUCCEEDED"},{"id":"autogen_task1_IF","status":"SUCCEEDED"},{"id":"autogen_task1_nao","status":"SUCCEEDED"},{"id":"autogen_task1_nai","status":"SUCCEEDED"},{"id":"autogen_task1_scale","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_Ena","status":"SUCCEEDED"},{"id":"autogen_task1_a11","status":"SUCCEEDED"},{"id":"autogen_task1_a12","status":"SUCCEEDED"},{"id":"autogen_task1_a13","status":"SUCCEEDED"},{"id":"autogen_task1_b11","status":"SUCCEEDED"},{"id":"autogen_task1_b12","status":"SUCCEEDED"},{"id":"autogen_task1_b13","status":"SUCCEEDED"},{"id":"autogen_task1_a2","status":"SUCCEEDED"},{"id":"autogen_task1_b2","status":"SUCCEEDED"},{"id":"autogen_task1_a3","status":"SUCCEEDED"},{"id":"autogen_task1_b3","status":"SUCCEEDED"},{"id":"autogen_task1_a4","status":"SUCCEEDED"},{"id":"autogen_task1_b4","status":"SUCCEEDED"},{"id":"autogen_task1_a5","status":"SUCCEEDED"},{"id":"autogen_task1_b5","status":"SUCCEEDED"},{"id":"autogen_task1_Gna","status":"SUCCEEDED"},{"id":"autogen_task1_Rk","status":"SUCCEEDED"},{"id":"autogen_task1_Fara","status":"SUCCEEDED"},{"id":"autogen_task1_Temp","status":"SUCCEEDED"},{"id":"autogen_task1_Ina","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000001","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000002","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000003","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000004","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000005","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000006","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000007","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000008","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000009","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000010","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000011","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.537751,"curves":[{"id":"autogen_curve_task1_C1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IC3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IC2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IM1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IM2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IF","status":"SUCCEEDED"}]}]}]}