{"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    459      0 --:--:-- --:--:-- --:--:--   460\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  289k  100  289k    0     0   669k      0 --:--:-- --:--:-- --:--:-- 3533k\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/64711c590dcacb55678cc809/rawLog.txt\nCompleted 4.5 KiB/4.5 KiB (66.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/MODEL1006230091.sedml/ (stored 0%)\n  adding: outputs/MODEL1006230091.sedml/plot_1_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 18%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 150.9 KiB/150.9 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/outputs/reports.h5\nCompleted 135.6 KiB/160.1 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/output.zip\nCompleted 135.6 KiB/160.1 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 144.5 KiB/160.1 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/outputs/plots.zip\nCompleted 144.5 KiB/160.1 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 157.4 KiB/160.1 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: outputs/MODEL1006230091.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/outputs/MODEL1006230091.sedml/plot_1_task1.pdf\nCompleted 157.4 KiB/160.1 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 160.1 KiB/160.1 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000698-biopax2.owl  \n  inflating: contents/BIOMD0000000698-biopax3.owl  \n  inflating: contents/BIOMD0000000698-matlab.m  \n  inflating: contents/BIOMD0000000698-octave.m  \n  inflating: contents/BIOMD0000000698.m  \n  inflating: contents/BIOMD0000000698.ode  \n  inflating: contents/BIOMD0000000698.pdf  \n  inflating: contents/BIOMD0000000698.png  \n  inflating: contents/BIOMD0000000698.svg  \n  inflating: contents/BIOMD0000000698.vcml  \n  inflating: contents/BIOMD0000000698_url.xml  \n  inflating: contents/MODEL1006230091.cps  \n  inflating: contents/MODEL1006230091.sedml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 27.7 KiB/599.4 KiB (392.6 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000698-biopax3.owl to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698-biopax3.owl\nCompleted 27.7 KiB/599.4 KiB (392.6 KiB/s) with 16 file(s) remaining\rCompleted 35.5 KiB/599.4 KiB (296.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000698-octave.m to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698-octave.m\nCompleted 35.5 KiB/599.4 KiB (296.0 KiB/s) with 15 file(s) remaining\rCompleted 55.1 KiB/599.4 KiB (430.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000698-biopax2.owl to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698-biopax2.owl\nCompleted 55.1 KiB/599.4 KiB (430.1 KiB/s) with 14 file(s) remaining\rCompleted 55.2 KiB/599.4 KiB (416.9 KiB/s) with 14 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/curation_notes.txt\nCompleted 55.2 KiB/599.4 KiB (416.9 KiB/s) with 13 file(s) remaining\rCompleted 73.9 KiB/599.4 KiB (543.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000698.svg to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698.svg\nCompleted 73.9 KiB/599.4 KiB (543.2 KiB/s) with 12 file(s) remaining\rCompleted 81.8 KiB/599.4 KiB (591.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000698-matlab.m to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698-matlab.m\nCompleted 81.8 KiB/599.4 KiB (591.5 KiB/s) with 11 file(s) remaining\rCompleted 147.5 KiB/599.4 KiB (1014.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000698.vcml to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698.vcml\nCompleted 147.5 KiB/599.4 KiB (1014.8 KiB/s) with 10 file(s) remaining\rCompleted 211.2 KiB/599.4 KiB (1.3 MiB/s) with 10 file(s) remaining   \rupload: contents/BIOMD0000000698_url.xml to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698_url.xml\nCompleted 211.2 KiB/599.4 KiB (1.3 MiB/s) with 9 file(s) remaining\rCompleted 233.8 KiB/599.4 KiB (1.4 MiB/s) with 9 file(s) remaining\rupload: contents/MODEL1006230091.sedml to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/MODEL1006230091.sedml\nCompleted 233.8 KiB/599.4 KiB (1.4 MiB/s) with 8 file(s) remaining\rCompleted 256.4 KiB/599.4 KiB (1.5 MiB/s) with 8 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/curation_image.jpeg\nCompleted 256.4 KiB/599.4 KiB (1.5 MiB/s) with 7 file(s) remaining\rCompleted 337.8 KiB/599.4 KiB (1.8 MiB/s) with 7 file(s) remaining\rupload: contents/MODEL1006230091.cps to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/MODEL1006230091.cps\nCompleted 337.8 KiB/599.4 KiB (1.8 MiB/s) with 6 file(s) remaining\rCompleted 339.8 KiB/599.4 KiB (1.8 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/manifest.xml\nCompleted 339.8 KiB/599.4 KiB (1.8 MiB/s) with 5 file(s) remaining\rCompleted 346.1 KiB/599.4 KiB (1.7 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000698.ode to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698.ode\nCompleted 346.1 KiB/599.4 KiB (1.7 MiB/s) with 4 file(s) remaining\rCompleted 350.5 KiB/599.4 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/metadata.rdf\nCompleted 350.5 KiB/599.4 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 358.4 KiB/599.4 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000698.m to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698.m\nCompleted 358.4 KiB/599.4 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 544.8 KiB/599.4 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000698.pdf to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698.pdf\nCompleted 544.8 KiB/599.4 KiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 599.4 KiB/599.4 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000698.png to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/contents/BIOMD0000000698.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (144.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c590dcacb55678cc809/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /MODEL1006230091.sedml\ncreating dataset /MODEL1006230091.sedml/autogen_report_for_task1, shape: (40, 1001), type: float64\ndataset created, uuid: d-08b42273-bc0f77ea-52a3-308139-714d55, chunk_size: (40, 1001)\ncreating dataset /MODEL1006230091.sedml/plot_1_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-08b42273-bc0f77ea-b179-0ca641-3905fc, chunk_size: (5, 1001)\ncreating attribute combineArchiveLocation in /MODEL1006230091.sedml\ncreating attribute uri in /MODEL1006230091.sedml\ncreating attribute _type in /MODEL1006230091.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1006230091.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /MODEL1006230091.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /MODEL1006230091.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /MODEL1006230091.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /MODEL1006230091.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /MODEL1006230091.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /MODEL1006230091.sedml/autogen_report_for_task1\ncreating attribute uri in /MODEL1006230091.sedml/autogen_report_for_task1\ncreating attribute _type in /MODEL1006230091.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1006230091.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /MODEL1006230091.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /MODEL1006230091.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /MODEL1006230091.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /MODEL1006230091.sedml/plot_1_task1\ncreating attribute sedmlId in /MODEL1006230091.sedml/plot_1_task1\ncreating attribute sedmlName in /MODEL1006230091.sedml/plot_1_task1\ncreating attribute uri in /MODEL1006230091.sedml/plot_1_task1\ncreate_links: /\ngot link: MODEL1006230091.sedml\ncreate_links: /MODEL1006230091.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /MODEL1006230091.sedml/autogen_report_for_task1 to tgt: /MODEL1006230091.sedml/autogen_report_for_task1, shape: (40, 1001), type: float64\niterating over chunks for /MODEL1006230091.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 40, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1006230091.sedml/autogen_report_for_task1\nwrite_dataset src: /MODEL1006230091.sedml/plot_1_task1 to tgt: /MODEL1006230091.sedml/plot_1_task1, shape: (5, 1001), type: float64\niterating over chunks for /MODEL1006230091.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1006230091.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c590dcacb55678cc809\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 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 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":1.391762,"sedDocuments":[{"location":"MODEL1006230091.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  MODEL1006230091.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 40 data sets\r\n    Plots (1):\r\n      plot_1_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: MODEL1006230091.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":0.99292,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.223246,"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":0.367304,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.258689,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_AdoMet","status":"SUCCEEDED"},{"id":"autogen_task1_Homocysteine","status":"SUCCEEDED"},{"id":"autogen_task1_Methionine","status":"SUCCEEDED"},{"id":"autogen_task1_Metin","status":"SUCCEEDED"},{"id":"autogen_task1_AdoHcy","status":"SUCCEEDED"},{"id":"autogen_task1__5mTHF","status":"SUCCEEDED"},{"id":"autogen_task1_Cystathionine","status":"SUCCEEDED"},{"id":"autogen_task1_V_max_MATI","status":"SUCCEEDED"},{"id":"autogen_task1_K_m_MATI","status":"SUCCEEDED"},{"id":"autogen_task1_K_i_MATI","status":"SUCCEEDED"},{"id":"autogen_task1_V_max_MATIII","status":"SUCCEEDED"},{"id":"autogen_task1_K_m1_MATIII","status":"SUCCEEDED"},{"id":"autogen_task1_K_m2_MATIII","status":"SUCCEEDED"},{"id":"autogen_task1_V_max_GNMT","status":"SUCCEEDED"},{"id":"autogen_task1_K_m_GNMT","status":"SUCCEEDED"},{"id":"autogen_task1_K_i_GNMT","status":"SUCCEEDED"},{"id":"autogen_task1_V_max_METH","status":"SUCCEEDED"},{"id":"autogen_task1_K_m1_METH","status":"SUCCEEDED"},{"id":"autogen_task1_K_m2_METH_A","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_2","status":"SUCCEEDED"},{"id":"autogen_task1_beta_1","status":"SUCCEEDED"},{"id":"autogen_task1_beta_2","status":"SUCCEEDED"},{"id":"autogen_task1_V_max_MS","status":"SUCCEEDED"},{"id":"autogen_task1_K_m_Hcy_MS","status":"SUCCEEDED"},{"id":"autogen_task1_K_m_5mTHF_MS","status":"SUCCEEDED"},{"id":"autogen_task1_K_d_MS","status":"SUCCEEDED"},{"id":"autogen_task1_V_max_BHMT","status":"SUCCEEDED"},{"id":"autogen_task1_K_m_BHMT","status":"SUCCEEDED"},{"id":"autogen_task1_Compartment","status":"SUCCEEDED"},{"id":"autogen_task1_V_MAT_I","status":"SUCCEEDED"},{"id":"autogen_task1_V_MAT_III","status":"SUCCEEDED"},{"id":"autogen_task1_V_METH","status":"SUCCEEDED"},{"id":"autogen_task1_V_GNMT","status":"SUCCEEDED"},{"id":"autogen_task1_V_AH","status":"SUCCEEDED"},{"id":"autogen_task1_V_MS","status":"SUCCEEDED"},{"id":"autogen_task1_V_BHMT","status":"SUCCEEDED"},{"id":"autogen_task1_V_CBS","status":"SUCCEEDED"},{"id":"autogen_task1_METIN","status":"SUCCEEDED"}]}]}]}