{"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    380      0 --:--:-- --:--:-- --:--:--   381\n\r100  297k  100  297k    0     0   615k      0 --:--:-- --:--:-- --:--:--  615k\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 (23.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/rawLog.txt\nCompleted 4.1 KiB/4.1 KiB (57.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/BIOMD0000000222_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000222_url.sedml/autogen_plot_for_task1.pdf (deflated 27%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 203.8 KiB/203.8 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/outputs/reports.h5\nCompleted 193.5 KiB/220.1 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/output.zip\nCompleted 193.5 KiB/220.1 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 203.5 KiB/220.1 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/outputs/plots.zip\nCompleted 203.5 KiB/220.1 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 206.1 KiB/220.1 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/rawLog.txt\nCompleted 206.1 KiB/220.1 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 220.1 KiB/220.1 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000222_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/outputs/BIOMD0000000222_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/BIOMD0000000222-biopax2.owl  \n  inflating: contents/BIOMD0000000222-biopax3.owl  \n  inflating: contents/BIOMD0000000222-matlab.m  \n  inflating: contents/BIOMD0000000222-octave.m  \n  inflating: contents/BIOMD0000000222.m  \n  inflating: contents/BIOMD0000000222.ode  \n  inflating: contents/BIOMD0000000222.pdf  \n  inflating: contents/BIOMD0000000222.png  \n  inflating: contents/BIOMD0000000222.svg  \n  inflating: contents/BIOMD0000000222.vcml  \n  inflating: contents/BIOMD0000000222_manual.png  \n  inflating: contents/BIOMD0000000222_manual.svg  \n  inflating: contents/BIOMD0000000222_url.sedml  \n  inflating: contents/BIOMD0000000222_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 27.0 KiB/612.8 KiB (401.3 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000222-biopax2.owl to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222-biopax2.owl\nCompleted 27.0 KiB/612.8 KiB (401.3 KiB/s) with 17 file(s) remaining\rCompleted 37.7 KiB/612.8 KiB (341.5 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000222-octave.m to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222-octave.m\nCompleted 37.7 KiB/612.8 KiB (341.5 KiB/s) with 16 file(s) remaining\rCompleted 48.3 KiB/612.8 KiB (388.3 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000222-matlab.m to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222-matlab.m\nCompleted 48.3 KiB/612.8 KiB (388.3 KiB/s) with 15 file(s) remaining\rCompleted 63.7 KiB/612.8 KiB (463.6 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000222.png to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222.png\nCompleted 63.7 KiB/612.8 KiB (463.6 KiB/s) with 14 file(s) remaining\rCompleted 164.5 KiB/612.8 KiB (1.1 MiB/s) with 14 file(s) remaining \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/curation_image.png\nCompleted 164.5 KiB/612.8 KiB (1.1 MiB/s) with 13 file(s) remaining\rCompleted 214.5 KiB/612.8 KiB (1.4 MiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000222.vcml to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222.vcml\nCompleted 214.5 KiB/612.8 KiB (1.4 MiB/s) with 12 file(s) remaining\rCompleted 230.0 KiB/612.8 KiB (1.4 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000222_manual.png to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222_manual.png\nCompleted 230.0 KiB/612.8 KiB (1.4 MiB/s) with 11 file(s) remaining\rCompleted 260.6 KiB/612.8 KiB (1.6 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000222.svg to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222.svg\nCompleted 260.6 KiB/612.8 KiB (1.6 MiB/s) with 10 file(s) remaining\rCompleted 291.2 KiB/612.8 KiB (1.7 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000222_manual.svg to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222_manual.svg\nCompleted 291.2 KiB/612.8 KiB (1.7 MiB/s) with 9 file(s) remaining\rCompleted 306.1 KiB/612.8 KiB (1.6 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000222_url.sedml to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222_url.sedml\nCompleted 306.1 KiB/612.8 KiB (1.6 MiB/s) with 8 file(s) remaining\rCompleted 308.1 KiB/612.8 KiB (1.6 MiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/manifest.xml\nCompleted 308.1 KiB/612.8 KiB (1.6 MiB/s) with 7 file(s) remaining\rCompleted 345.8 KiB/612.8 KiB (1.7 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000222-biopax3.owl to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222-biopax3.owl\nCompleted 345.8 KiB/612.8 KiB (1.7 MiB/s) with 6 file(s) remaining\rCompleted 392.3 KiB/612.8 KiB (1.8 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000222_url.xml to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222_url.xml\nCompleted 392.3 KiB/612.8 KiB (1.8 MiB/s) with 5 file(s) remaining\rCompleted 399.3 KiB/612.8 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000222.ode to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222.ode\nCompleted 399.3 KiB/612.8 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 404.3 KiB/612.8 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/metadata.rdf\nCompleted 404.3 KiB/612.8 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 414.9 KiB/612.8 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000222.m to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222.m\nCompleted 414.9 KiB/612.8 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 612.6 KiB/612.8 KiB (2.7 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000222.pdf to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/BIOMD0000000222.pdf\nCompleted 612.6 KiB/612.8 KiB (2.7 MiB/s) with 1 file(s) remaining\rCompleted 612.8 KiB/612.8 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/contents/curation_notes.txt\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.4 KiB/9.4 KiB (123.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109ce49c0d898ffdde3f7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000222_url.sedml\ncreating dataset /BIOMD0000000222_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\ndataset created, uuid: d-cafefc80-2ec775ef-e887-6ace70-be4251, chunk_size: (13, 1001)\ncreating dataset /BIOMD0000000222_url.sedml/autogen_report_for_task1, shape: (25, 1001), type: float64\ndataset created, uuid: d-cafefc80-2ec775ef-4c74-97a2ea-ef94ed, chunk_size: (25, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000222_url.sedml\ncreating attribute uri in /BIOMD0000000222_url.sedml\ncreating attribute _type in /BIOMD0000000222_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000222_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000222_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000222_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000222_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000222_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000222_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000222_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000222_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000222_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000222_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000222_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000222_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000222_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000222_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000222_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000222_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000222_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000222_url.sedml\ncreate_links: /BIOMD0000000222_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000222_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000222_url.sedml/autogen_plot_for_task1, shape: (13, 1001), type: float64\niterating over chunks for /BIOMD0000000222_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000222_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000222_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000222_url.sedml/autogen_report_for_task1, shape: (25, 1001), type: float64\niterating over chunks for /BIOMD0000000222_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 25, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000222_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647109ce49c0d898ffdde3f7\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 and upload the outputs of the simulation run ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.632364,"sedDocuments":[{"location":"BIOMD0000000222_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  BIOMD0000000222_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 25 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000222_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":1.108762,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.239689,"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":0.213747,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_aca","status":"SUCCEEDED"},{"id":"autogen_task1_oaa","status":"SUCCEEDED"},{"id":"autogen_task1_coa","status":"SUCCEEDED"},{"id":"autogen_task1_cit","status":"SUCCEEDED"},{"id":"autogen_task1_icit","status":"SUCCEEDED"},{"id":"autogen_task1_akg","status":"SUCCEEDED"},{"id":"autogen_task1_sca","status":"SUCCEEDED"},{"id":"autogen_task1_suc","status":"SUCCEEDED"},{"id":"autogen_task1_fa","status":"SUCCEEDED"},{"id":"autogen_task1_mal","status":"SUCCEEDED"},{"id":"autogen_task1_gly","status":"SUCCEEDED"},{"id":"autogen_task1_biosyn","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_CS","status":"SUCCEEDED"},{"id":"autogen_task1_ACN","status":"SUCCEEDED"},{"id":"autogen_task1_ICD","status":"SUCCEEDED"},{"id":"autogen_task1_KDH","status":"SUCCEEDED"},{"id":"autogen_task1_ScAS","status":"SUCCEEDED"},{"id":"autogen_task1_SDH","status":"SUCCEEDED"},{"id":"autogen_task1_FUM","status":"SUCCEEDED"},{"id":"autogen_task1_MDH","status":"SUCCEEDED"},{"id":"autogen_task1_ICL","status":"SUCCEEDED"},{"id":"autogen_task1_MS","status":"SUCCEEDED"},{"id":"autogen_task1_SYN","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.506714,"curves":[{"id":"autogen_curve_task1_aca","status":"SUCCEEDED"},{"id":"autogen_curve_task1_oaa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_coa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_cit","status":"SUCCEEDED"},{"id":"autogen_curve_task1_icit","status":"SUCCEEDED"},{"id":"autogen_curve_task1_akg","status":"SUCCEEDED"},{"id":"autogen_curve_task1_sca","status":"SUCCEEDED"},{"id":"autogen_curve_task1_suc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_fa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_mal","status":"SUCCEEDED"},{"id":"autogen_curve_task1_gly","status":"SUCCEEDED"},{"id":"autogen_curve_task1_biosyn","status":"SUCCEEDED"}]}]}]}