{"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  311k  100  311k    0     0   688k      0 --:--:-- --:--:-- --:--:--  688k\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/647109c40dcacb55678b84ac/rawLog.txt\nCompleted 4.4 KiB/4.4 KiB (52.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/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/BIOMD0000000219_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000219_url.sedml/autogen_plot_for_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 244.7 KiB/244.7 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/outputs/reports.h5\nCompleted 228.9 KiB/255.4 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/output.zip\nCompleted 228.9 KiB/255.4 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 231.5 KiB/255.4 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/rawLog.txt\nCompleted 231.5 KiB/255.4 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 241.5 KiB/255.4 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/outputs/plots.zip\nCompleted 241.5 KiB/255.4 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 255.4 KiB/255.4 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000219_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/outputs/BIOMD0000000219_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/BIOMD0000000219-biopax2.owl  \n  inflating: contents/BIOMD0000000219-biopax3.owl  \n  inflating: contents/BIOMD0000000219-matlab.m  \n  inflating: contents/BIOMD0000000219-octave.m  \n  inflating: contents/BIOMD0000000219.m  \n  inflating: contents/BIOMD0000000219.ode  \n  inflating: contents/BIOMD0000000219.pdf  \n  inflating: contents/BIOMD0000000219.png  \n  inflating: contents/BIOMD0000000219.svg  \n  inflating: contents/BIOMD0000000219.vcml  \n  inflating: contents/BIOMD0000000219_manual.png  \n  inflating: contents/BIOMD0000000219_manual.svg  \n  inflating: contents/BIOMD0000000219_url.sedml  \n  inflating: contents/BIOMD0000000219_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 46.3 KiB/692.6 KiB (488.5 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000219-biopax3.owl to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219-biopax3.owl\nCompleted 46.3 KiB/692.6 KiB (488.5 KiB/s) with 17 file(s) remaining\rCompleted 78.7 KiB/692.6 KiB (606.5 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000219-biopax2.owl to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219-biopax2.owl\nCompleted 78.7 KiB/692.6 KiB (606.5 KiB/s) with 16 file(s) remaining\rCompleted 92.7 KiB/692.6 KiB (691.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000219-octave.m to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219-octave.m\nCompleted 92.7 KiB/692.6 KiB (691.5 KiB/s) with 15 file(s) remaining\rCompleted 127.4 KiB/692.6 KiB (749.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000219.svg to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219.svg\nCompleted 127.4 KiB/692.6 KiB (749.3 KiB/s) with 14 file(s) remaining\rCompleted 222.4 KiB/692.6 KiB (1.3 MiB/s) with 14 file(s) remaining  \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/curation_image.png\nCompleted 222.4 KiB/692.6 KiB (1.3 MiB/s) with 13 file(s) remaining\rCompleted 283.3 KiB/692.6 KiB (1.6 MiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000219.vcml to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219.vcml\nCompleted 283.3 KiB/692.6 KiB (1.6 MiB/s) with 12 file(s) remaining\rCompleted 299.8 KiB/692.6 KiB (1.6 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000219_manual.png to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219_manual.png\nCompleted 299.8 KiB/692.6 KiB (1.6 MiB/s) with 11 file(s) remaining\rCompleted 300.1 KiB/692.6 KiB (1.6 MiB/s) with 11 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/curation_notes.txt\nCompleted 300.1 KiB/692.6 KiB (1.6 MiB/s) with 10 file(s) remaining\rCompleted 334.7 KiB/692.6 KiB (1.7 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000219_manual.svg to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219_manual.svg\nCompleted 334.7 KiB/692.6 KiB (1.7 MiB/s) with 9 file(s) remaining\rCompleted 352.1 KiB/692.6 KiB (1.8 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000219_url.sedml to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219_url.sedml\nCompleted 352.1 KiB/692.6 KiB (1.8 MiB/s) with 8 file(s) remaining\rCompleted 354.2 KiB/692.6 KiB (1.8 MiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/manifest.xml\nCompleted 354.2 KiB/692.6 KiB (1.8 MiB/s) with 7 file(s) remaining\rCompleted 414.8 KiB/692.6 KiB (1.9 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000219_url.xml to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219_url.xml\nCompleted 414.8 KiB/692.6 KiB (1.9 MiB/s) with 6 file(s) remaining\rCompleted 428.8 KiB/692.6 KiB (1.7 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000219-matlab.m to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219-matlab.m\nCompleted 428.8 KiB/692.6 KiB (1.7 MiB/s) with 5 file(s) remaining\rCompleted 433.7 KiB/692.6 KiB (1.7 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/metadata.rdf\nCompleted 433.7 KiB/692.6 KiB (1.7 MiB/s) with 4 file(s) remaining\rCompleted 447.7 KiB/692.6 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000219.m to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219.m\nCompleted 447.7 KiB/692.6 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 457.1 KiB/692.6 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000219.ode to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219.ode\nCompleted 457.1 KiB/692.6 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 473.7 KiB/692.6 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000219.png to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219.png\nCompleted 473.7 KiB/692.6 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 692.6 KiB/692.6 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000219.pdf to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/contents/BIOMD0000000219.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.4 KiB/9.4 KiB (141.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109c40dcacb55678b84ac/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000219_url.sedml\ncreating dataset /BIOMD0000000219_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-31183853-f9b7aa2f-0d3e-613c84-ee126c, chunk_size: (14, 1001)\ncreating dataset /BIOMD0000000219_url.sedml/autogen_report_for_task1, shape: (30, 1001), type: float64\ndataset created, uuid: d-31183853-f9b7aa2f-9f02-d84539-7ae875, chunk_size: (30, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000219_url.sedml\ncreating attribute uri in /BIOMD0000000219_url.sedml\ncreating attribute _type in /BIOMD0000000219_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000219_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000219_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000219_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000219_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000219_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000219_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000219_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000219_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000219_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000219_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000219_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000219_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000219_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000219_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000219_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000219_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000219_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000219_url.sedml\ncreate_links: /BIOMD0000000219_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000219_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000219_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000219_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000219_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000219_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000219_url.sedml/autogen_report_for_task1, shape: (30, 1001), type: float64\niterating over chunks for /BIOMD0000000219_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 30, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000219_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647109c40dcacb55678b84ac\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve 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.\nProcess 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.837321,"sedDocuments":[{"location":"BIOMD0000000219_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  BIOMD0000000219_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 30 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 13 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000219_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":1.330512,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.282693,"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":0.259928,"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_ssa","status":"SUCCEEDED"},{"id":"autogen_task1_suc","status":"SUCCEEDED"},{"id":"autogen_task1_sca","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_ICD1","status":"SUCCEEDED"},{"id":"autogen_task1_ICD2","status":"SUCCEEDED"},{"id":"autogen_task1_KDH","status":"SUCCEEDED"},{"id":"autogen_task1_KGD","status":"SUCCEEDED"},{"id":"autogen_task1_SSADH","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_ICL1","status":"SUCCEEDED"},{"id":"autogen_task1_ICL2","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":0.621989,"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_ssa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_suc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_sca","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"}]}]}]}