{"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    457      0 --:--:-- --:--:-- --:--:--   458\n\r100  186k  100  186k    0     0   443k      0 --:--:-- --:--:-- --:--:--  443k\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 (24.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/rawLog.txt\nCompleted 3.6 KiB/3.6 KiB (47.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/MODEL1708250001.sedml/ (stored 0%)\n  adding: outputs/MODEL1708250001.sedml/plot_1_task1.pdf (deflated 26%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/reports.h5 (deflated 16%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 133.1 KiB/133.1 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/outputs/reports.h5\nCompleted 125.5 KiB/154.9 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/output.zip\nCompleted 125.5 KiB/154.9 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 136.7 KiB/154.9 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/outputs/plots.zip\nCompleted 136.7 KiB/154.9 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 152.3 KiB/154.9 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: outputs/MODEL1708250001.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/outputs/MODEL1708250001.sedml/plot_1_task1.pdf\nCompleted 152.3 KiB/154.9 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 154.9 KiB/154.9 KiB (983.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000671-biopax2.owl  \n  inflating: contents/BIOMD0000000671-biopax3.owl  \n  inflating: contents/BIOMD0000000671-matlab.m  \n  inflating: contents/BIOMD0000000671-octave.m  \n  inflating: contents/BIOMD0000000671.m  \n  inflating: contents/BIOMD0000000671.ode  \n  inflating: contents/BIOMD0000000671.pdf  \n  inflating: contents/BIOMD0000000671.png  \n  inflating: contents/BIOMD0000000671.svg  \n  inflating: contents/BIOMD0000000671_url.xml  \n  inflating: contents/MODEL1708250001.cps  \n  inflating: contents/MODEL1708250001.sedml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 4.4 KiB/294.0 KiB (68.3 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000671-biopax2.owl to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/BIOMD0000000671-biopax2.owl\nCompleted 4.4 KiB/294.0 KiB (68.3 KiB/s) with 15 file(s) remaining\rCompleted 9.1 KiB/294.0 KiB (82.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000671-octave.m to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/BIOMD0000000671-octave.m\nCompleted 9.1 KiB/294.0 KiB (82.9 KiB/s) with 14 file(s) remaining\rCompleted 9.9 KiB/294.0 KiB (87.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000671.svg to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/BIOMD0000000671.svg\nCompleted 9.9 KiB/294.0 KiB (87.6 KiB/s) with 13 file(s) remaining\rCompleted 14.7 KiB/294.0 KiB (128.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000671-matlab.m to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/BIOMD0000000671-matlab.m\nCompleted 14.7 KiB/294.0 KiB (128.2 KiB/s) with 12 file(s) remaining\rCompleted 14.8 KiB/294.0 KiB (116.7 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/curation_notes.txt\nCompleted 14.8 KiB/294.0 KiB (116.7 KiB/s) with 11 file(s) remaining\rCompleted 19.1 KiB/294.0 KiB (142.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000671.png to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/BIOMD0000000671.png\nCompleted 19.1 KiB/294.0 KiB (142.3 KiB/s) with 10 file(s) remaining\rCompleted 46.8 KiB/294.0 KiB (325.3 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000671_url.xml to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/BIOMD0000000671_url.xml\nCompleted 46.8 KiB/294.0 KiB (325.3 KiB/s) with 9 file(s) remaining\rCompleted 60.8 KiB/294.0 KiB (382.6 KiB/s) with 9 file(s) remaining\rupload: contents/MODEL1708250001.sedml to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/MODEL1708250001.sedml\nCompleted 60.8 KiB/294.0 KiB (382.6 KiB/s) with 8 file(s) remaining\rCompleted 111.6 KiB/294.0 KiB (666.6 KiB/s) with 8 file(s) remaining\rupload: contents/MODEL1708250001.cps to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/MODEL1708250001.cps\nCompleted 111.6 KiB/294.0 KiB (666.6 KiB/s) with 7 file(s) remaining\rCompleted 116.7 KiB/294.0 KiB (685.3 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000671-biopax3.owl to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/BIOMD0000000671-biopax3.owl\nCompleted 116.7 KiB/294.0 KiB (685.3 KiB/s) with 6 file(s) remaining\rCompleted 121.2 KiB/294.0 KiB (697.6 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/metadata.rdf\nCompleted 121.2 KiB/294.0 KiB (697.6 KiB/s) with 5 file(s) remaining\rCompleted 147.7 KiB/294.0 KiB (834.4 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/curation_image.png\nCompleted 147.7 KiB/294.0 KiB (834.4 KiB/s) with 4 file(s) remaining\rCompleted 152.4 KiB/294.0 KiB (795.4 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000671.m to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/BIOMD0000000671.m\nCompleted 152.4 KiB/294.0 KiB (795.4 KiB/s) with 3 file(s) remaining\rCompleted 289.5 KiB/294.0 KiB (1.5 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000671.pdf to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/BIOMD0000000671.pdf\nCompleted 289.5 KiB/294.0 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 291.3 KiB/294.0 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/manifest.xml\nCompleted 291.3 KiB/294.0 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 294.0 KiB/294.0 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000671.ode to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/contents/BIOMD0000000671.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.7 KiB/8.7 KiB (137.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711c039a62a8be53f8cc0b/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /MODEL1708250001.sedml\ncreating dataset /MODEL1708250001.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\ndataset created, uuid: d-a0d47bec-19d8cc26-e9ec-ddbb44-985ac8, chunk_size: (23, 1001)\ncreating dataset /MODEL1708250001.sedml/plot_1_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-a0d47bec-19d8cc26-607f-90fd43-c19aac, chunk_size: (8, 1001)\ncreating attribute combineArchiveLocation in /MODEL1708250001.sedml\ncreating attribute uri in /MODEL1708250001.sedml\ncreating attribute _type in /MODEL1708250001.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1708250001.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /MODEL1708250001.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /MODEL1708250001.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /MODEL1708250001.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /MODEL1708250001.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /MODEL1708250001.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /MODEL1708250001.sedml/autogen_report_for_task1\ncreating attribute uri in /MODEL1708250001.sedml/autogen_report_for_task1\ncreating attribute _type in /MODEL1708250001.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /MODEL1708250001.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /MODEL1708250001.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /MODEL1708250001.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /MODEL1708250001.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /MODEL1708250001.sedml/plot_1_task1\ncreating attribute sedmlId in /MODEL1708250001.sedml/plot_1_task1\ncreating attribute sedmlName in /MODEL1708250001.sedml/plot_1_task1\ncreating attribute uri in /MODEL1708250001.sedml/plot_1_task1\ncreate_links: /\ngot link: MODEL1708250001.sedml\ncreate_links: /MODEL1708250001.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /MODEL1708250001.sedml/autogen_report_for_task1 to tgt: /MODEL1708250001.sedml/autogen_report_for_task1, shape: (23, 1001), type: float64\niterating over chunks for /MODEL1708250001.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 23, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1708250001.sedml/autogen_report_for_task1\nwrite_dataset src: /MODEL1708250001.sedml/plot_1_task1 to tgt: /MODEL1708250001.sedml/plot_1_task1, shape: (8, 1001), type: float64\niterating over chunks for /MODEL1708250001.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /MODEL1708250001.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711c039a62a8be53f8cc0b\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 the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.469571,"sedDocuments":[{"location":"MODEL1708250001.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  MODEL1708250001.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 23 data sets\r\n    Plots (1):\r\n      plot_1_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: MODEL1708250001.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":0.979762,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.199792,"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":0.45862,"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":"p1_curve_5_task1","status":"SUCCEEDED"},{"id":"p1_curve_6_task1","status":"SUCCEEDED"},{"id":"p1_curve_7_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.181026,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_V_bert","status":"SUCCEEDED"},{"id":"autogen_task1_V_exp","status":"SUCCEEDED"},{"id":"autogen_task1_V_gomp","status":"SUCCEEDED"},{"id":"autogen_task1_V_lin","status":"SUCCEEDED"},{"id":"autogen_task1_V_log","status":"SUCCEEDED"},{"id":"autogen_task1_V_mend","status":"SUCCEEDED"},{"id":"autogen_task1_V_surf","status":"SUCCEEDED"},{"id":"autogen_task1_a_exp","status":"SUCCEEDED"},{"id":"autogen_task1_a_mend","status":"SUCCEEDED"},{"id":"autogen_task1_a_log","status":"SUCCEEDED"},{"id":"autogen_task1_a_lin","status":"SUCCEEDED"},{"id":"autogen_task1_a_surf","status":"SUCCEEDED"},{"id":"autogen_task1_a_gomp","status":"SUCCEEDED"},{"id":"autogen_task1_a_bert","status":"SUCCEEDED"},{"id":"autogen_task1_b_mend","status":"SUCCEEDED"},{"id":"autogen_task1_b_log","status":"SUCCEEDED"},{"id":"autogen_task1_b_lin","status":"SUCCEEDED"},{"id":"autogen_task1_b_surf","status":"SUCCEEDED"},{"id":"autogen_task1_b_gomp","status":"SUCCEEDED"},{"id":"autogen_task1_b_bert","status":"SUCCEEDED"},{"id":"autogen_task1_c_gomp","status":"SUCCEEDED"},{"id":"autogen_task1_tumour","status":"SUCCEEDED"}]}]}]}