{"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    429      0 --:--:-- --:--:-- --:--:--   429\n\r100  321k  100  321k    0     0   705k      0 --:--:-- --:--:-- --:--:--  705k\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 (25.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/rawLog.txt\nCompleted 5.0 KiB/5.0 KiB (68.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/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/BIOMD0000000190_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000190_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 252.9 KiB/252.9 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/outputs/reports.h5\nCompleted 12.5 KiB/258.9 KiB (113.9 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000190_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/outputs/BIOMD0000000190_url.sedml/autogen_plot_for_task1.pdf\nCompleted 12.5 KiB/258.9 KiB (113.9 KiB/s) with 3 file(s) remaining\rCompleted 15.2 KiB/258.9 KiB (120.4 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/rawLog.txt\nCompleted 15.2 KiB/258.9 KiB (120.4 KiB/s) with 2 file(s) remaining\rCompleted 23.8 KiB/258.9 KiB (170.1 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/outputs/plots.zip\nCompleted 23.8 KiB/258.9 KiB (170.1 KiB/s) with 1 file(s) remaining\rCompleted 258.9 KiB/258.9 KiB (922.4 KiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000190-biopax2.owl  \n  inflating: contents/BIOMD0000000190-biopax3.owl  \n  inflating: contents/BIOMD0000000190-matlab.m  \n  inflating: contents/BIOMD0000000190-octave.m  \n  inflating: contents/BIOMD0000000190.m  \n  inflating: contents/BIOMD0000000190.ode  \n  inflating: contents/BIOMD0000000190.pdf  \n  inflating: contents/BIOMD0000000190.png  \n  inflating: contents/BIOMD0000000190.svg  \n  inflating: contents/BIOMD0000000190_url.sedml  \n  inflating: contents/BIOMD0000000190_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 44.4 KiB/613.0 KiB (559.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000190-biopax3.owl to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190-biopax3.owl\nCompleted 44.4 KiB/613.0 KiB (559.1 KiB/s) with 14 file(s) remaining\rCompleted 56.6 KiB/613.0 KiB (481.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000190-matlab.m to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190-matlab.m\nCompleted 56.6 KiB/613.0 KiB (481.9 KiB/s) with 13 file(s) remaining\rCompleted 68.9 KiB/613.0 KiB (506.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000190-octave.m to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190-octave.m\nCompleted 68.9 KiB/613.0 KiB (506.2 KiB/s) with 12 file(s) remaining\rCompleted 101.0 KiB/613.0 KiB (731.6 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000190-biopax2.owl to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190-biopax2.owl\nCompleted 101.0 KiB/613.0 KiB (731.6 KiB/s) with 11 file(s) remaining\rCompleted 130.7 KiB/613.0 KiB (928.2 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000190.svg to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190.svg\nCompleted 130.7 KiB/613.0 KiB (928.2 KiB/s) with 10 file(s) remaining\rCompleted 135.7 KiB/613.0 KiB (950.5 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/metadata.rdf\nCompleted 135.7 KiB/613.0 KiB (950.5 KiB/s) with 9 file(s) remaining\rCompleted 159.4 KiB/613.0 KiB (1001.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000190_url.sedml to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190_url.sedml\nCompleted 159.4 KiB/613.0 KiB (1001.0 KiB/s) with 8 file(s) remaining\rCompleted 172.0 KiB/613.0 KiB (1.0 MiB/s) with 8 file(s) remaining   \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/curation_image.png\nCompleted 172.0 KiB/613.0 KiB (1.0 MiB/s) with 7 file(s) remaining\rCompleted 172.2 KiB/613.0 KiB (1.0 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/curation_notes.txt\nCompleted 172.2 KiB/613.0 KiB (1.0 MiB/s) with 6 file(s) remaining\rCompleted 174.0 KiB/613.0 KiB (913.8 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/manifest.xml\nCompleted 174.0 KiB/613.0 KiB (913.8 KiB/s) with 5 file(s) remaining\rCompleted 230.0 KiB/613.0 KiB (1.2 MiB/s) with 5 file(s) remaining  \rupload: contents/BIOMD0000000190_url.xml to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190_url.xml\nCompleted 230.0 KiB/613.0 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 368.7 KiB/613.0 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000190.png to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190.png\nCompleted 368.7 KiB/613.0 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 376.7 KiB/613.0 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000190.ode to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190.ode\nCompleted 376.7 KiB/613.0 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 388.9 KiB/613.0 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000190.m to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190.m\nCompleted 388.9 KiB/613.0 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 613.0 KiB/613.0 KiB (2.6 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000190.pdf to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/contents/BIOMD0000000190.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (86.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471096449c0d898ffddd55c/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000190_url.sedml\ncreating dataset /BIOMD0000000190_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-003cc168-e72f8746-1133-684a20-72fdd6, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000190_url.sedml/autogen_report_for_task1, shape: (43, 1001), type: float64\ndataset created, uuid: d-003cc168-e72f8746-caa7-8235d8-921a96, chunk_size: (43, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000190_url.sedml\ncreating attribute uri in /BIOMD0000000190_url.sedml\ncreating attribute _type in /BIOMD0000000190_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000190_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000190_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000190_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000190_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000190_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000190_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000190_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000190_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000190_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000190_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000190_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000190_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000190_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000190_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000190_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000190_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000190_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000190_url.sedml\ncreate_links: /BIOMD0000000190_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000190_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000190_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000190_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000190_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000190_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000190_url.sedml/autogen_report_for_task1, shape: (43, 1001), type: float64\niterating over chunks for /BIOMD0000000190_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 43, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000190_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471096449c0d898ffddd55c\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.\nRetrieve 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 and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.920273,"sedDocuments":[{"location":"BIOMD0000000190_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  BIOMD0000000190_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 43 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000190_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":1.400373,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.293554,"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":0.339086,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_SAM","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_D","status":"SUCCEEDED"},{"id":"autogen_task1_aS","status":"SUCCEEDED"},{"id":"autogen_task1_aD","status":"SUCCEEDED"},{"id":"autogen_task1_Met","status":"SUCCEEDED"},{"id":"autogen_task1_ORN","status":"SUCCEEDED"},{"id":"autogen_task1_AcCoA","status":"SUCCEEDED"},{"id":"autogen_task1_CoA","status":"SUCCEEDED"},{"id":"autogen_task1_Vmaxodc","status":"SUCCEEDED"},{"id":"autogen_task1_Vmaxssat","status":"SUCCEEDED"},{"id":"autogen_task1_Vmaxsamdc","status":"SUCCEEDED"},{"id":"autogen_task1_Antz","status":"SUCCEEDED"},{"id":"autogen_task1_Keq","status":"SUCCEEDED"},{"id":"autogen_task1_Kdodc","status":"SUCCEEDED"},{"id":"autogen_task1_Ksodc","status":"SUCCEEDED"},{"id":"autogen_task1_Kdssat","status":"SUCCEEDED"},{"id":"autogen_task1_Ksssat","status":"SUCCEEDED"},{"id":"autogen_task1_Kdsamdc","status":"SUCCEEDED"},{"id":"autogen_task1_Kssamdc","status":"SUCCEEDED"},{"id":"autogen_task1_Kdantz","status":"SUCCEEDED"},{"id":"autogen_task1_Ksantz","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_Kaccoa","status":"SUCCEEDED"},{"id":"autogen_task1_Kcoa","status":"SUCCEEDED"},{"id":"autogen_task1_cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_ODC","status":"SUCCEEDED"},{"id":"autogen_task1_SAMdc","status":"SUCCEEDED"},{"id":"autogen_task1_SSAT_for_S","status":"SUCCEEDED"},{"id":"autogen_task1_SSAT_for_D","status":"SUCCEEDED"},{"id":"autogen_task1_PAO_for_aD","status":"SUCCEEDED"},{"id":"autogen_task1_PAO_for_aS","status":"SUCCEEDED"},{"id":"autogen_task1_SpdS","status":"SUCCEEDED"},{"id":"autogen_task1_SpmS","status":"SUCCEEDED"},{"id":"autogen_task1_MAT","status":"SUCCEEDED"},{"id":"autogen_task1_VCoA","status":"SUCCEEDED"},{"id":"autogen_task1_VacCoA","status":"SUCCEEDED"},{"id":"autogen_task1_P_efflux","status":"SUCCEEDED"},{"id":"autogen_task1_aD_efflux","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.593739,"curves":[{"id":"autogen_curve_task1_SAM","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S","status":"SUCCEEDED"},{"id":"autogen_curve_task1_D","status":"SUCCEEDED"},{"id":"autogen_curve_task1_aS","status":"SUCCEEDED"},{"id":"autogen_curve_task1_aD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Met","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ORN","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcCoA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CoA","status":"SUCCEEDED"}]}]}]}