{"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    451      0 --:--:-- --:--:-- --:--:--   452\n\r100  141k  100  141k    0     0   333k      0 --:--:-- --:--:-- --:--:--  333k\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 (8.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/rawLog.txt\nCompleted 4.4 KiB/4.4 KiB (63.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/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/BIOMD0000000138_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000138_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 18%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 146.2 KiB/146.2 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/outputs/reports.h5\nCompleted 130.9 KiB/153.3 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/output.zip\nCompleted 130.9 KiB/153.3 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 138.8 KiB/153.3 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/outputs/plots.zip\nCompleted 138.8 KiB/153.3 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 150.7 KiB/153.3 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000138_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/outputs/BIOMD0000000138_url.sedml/autogen_plot_for_task1.pdf\nCompleted 150.7 KiB/153.3 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 153.3 KiB/153.3 KiB (782.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000138-biopax2.owl  \n  inflating: contents/BIOMD0000000138-biopax3.owl  \n  inflating: contents/BIOMD0000000138-matlab.m  \n  inflating: contents/BIOMD0000000138-octave.m  \n  inflating: contents/BIOMD0000000138.m  \n  inflating: contents/BIOMD0000000138.ode  \n  inflating: contents/BIOMD0000000138.pdf  \n  inflating: contents/BIOMD0000000138.png  \n  inflating: contents/BIOMD0000000138.svg  \n  inflating: contents/BIOMD0000000138_url.sedml  \n  inflating: contents/BIOMD0000000138_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 6.8 KiB/244.2 KiB (106.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000138-biopax3.owl to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138-biopax3.owl\nCompleted 6.8 KiB/244.2 KiB (106.3 KiB/s) with 14 file(s) remaining\rCompleted 12.9 KiB/244.2 KiB (125.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000138-matlab.m to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138-matlab.m\nCompleted 12.9 KiB/244.2 KiB (125.4 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000138.svg to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138.svg\nCompleted 12.9 KiB/244.2 KiB (125.4 KiB/s) with 12 file(s) remaining\rCompleted 19.0 KiB/244.2 KiB (157.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000138-biopax2.owl to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138-biopax2.owl\nCompleted 19.0 KiB/244.2 KiB (157.8 KiB/s) with 11 file(s) remaining\rCompleted 20.7 KiB/244.2 KiB (167.9 KiB/s) with 11 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/manifest.xml\nCompleted 20.7 KiB/244.2 KiB (167.9 KiB/s) with 10 file(s) remaining\rCompleted 26.8 KiB/244.2 KiB (203.5 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000138-octave.m to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138-octave.m\nCompleted 26.8 KiB/244.2 KiB (203.5 KiB/s) with 9 file(s) remaining\rCompleted 46.0 KiB/244.2 KiB (293.3 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000138_url.xml to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138_url.xml\nCompleted 46.0 KiB/244.2 KiB (293.3 KiB/s) with 8 file(s) remaining\rCompleted 68.1 KiB/244.2 KiB (428.4 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000138_url.sedml to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138_url.sedml\nCompleted 68.1 KiB/244.2 KiB (428.4 KiB/s) with 7 file(s) remaining\rCompleted 73.8 KiB/244.2 KiB (438.4 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/curation_image.png\nCompleted 73.8 KiB/244.2 KiB (438.4 KiB/s) with 6 file(s) remaining\rCompleted 79.9 KiB/244.2 KiB (467.1 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000138.m to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138.m\nCompleted 79.9 KiB/244.2 KiB (467.1 KiB/s) with 5 file(s) remaining\rCompleted 85.9 KiB/244.2 KiB (493.2 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000138.png to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138.png\nCompleted 85.9 KiB/244.2 KiB (493.2 KiB/s) with 4 file(s) remaining\rCompleted 237.0 KiB/244.2 KiB (1.3 MiB/s) with 4 file(s) remaining \rupload: contents/BIOMD0000000138.pdf to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138.pdf\nCompleted 237.0 KiB/244.2 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 237.0 KiB/244.2 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/curation_notes.txt\nCompleted 237.0 KiB/244.2 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 241.2 KiB/244.2 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000138.ode to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/BIOMD0000000138.ode\nCompleted 241.2 KiB/244.2 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 244.2 KiB/244.2 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.4 KiB/8.4 KiB (126.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108b69a62a8be53f7679d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000138_url.sedml\ncreating dataset /BIOMD0000000138_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-d3dd4395-050fb6da-73ce-fd2dd4-c80e45, chunk_size: (2, 1001)\ncreating dataset /BIOMD0000000138_url.sedml/autogen_report_for_task1, shape: (44, 1001), type: float64\ndataset created, uuid: d-d3dd4395-050fb6da-42d8-55877f-2651e2, chunk_size: (44, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000138_url.sedml\ncreating attribute uri in /BIOMD0000000138_url.sedml\ncreating attribute _type in /BIOMD0000000138_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000138_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000138_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000138_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000138_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000138_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000138_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000138_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000138_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000138_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000138_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000138_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000138_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000138_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000138_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000138_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000138_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000138_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000138_url.sedml\ncreate_links: /BIOMD0000000138_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000138_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000138_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\niterating over chunks for /BIOMD0000000138_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000138_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000138_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000138_url.sedml/autogen_report_for_task1, shape: (44, 1001), type: float64\niterating over chunks for /BIOMD0000000138_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 44, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000138_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647108b69a62a8be53f7679d\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.\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.559064,"sedDocuments":[{"location":"BIOMD0000000138_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  BIOMD0000000138_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 44 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000138_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":1.089849,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.248852,"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":0.328966,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_vca","status":"SUCCEEDED"},{"id":"autogen_task1_vk","status":"SUCCEEDED"},{"id":"autogen_task1_Cm","status":"SUCCEEDED"},{"id":"autogen_task1_gk","status":"SUCCEEDED"},{"id":"autogen_task1_gcal","status":"SUCCEEDED"},{"id":"autogen_task1_gsk","status":"SUCCEEDED"},{"id":"autogen_task1_ga","status":"SUCCEEDED"},{"id":"autogen_task1_gf","status":"SUCCEEDED"},{"id":"autogen_task1_vn","status":"SUCCEEDED"},{"id":"autogen_task1_va","status":"SUCCEEDED"},{"id":"autogen_task1_vm","status":"SUCCEEDED"},{"id":"autogen_task1_vh","status":"SUCCEEDED"},{"id":"autogen_task1_vf","status":"SUCCEEDED"},{"id":"autogen_task1_sn","status":"SUCCEEDED"},{"id":"autogen_task1_sa","status":"SUCCEEDED"},{"id":"autogen_task1_sm","status":"SUCCEEDED"},{"id":"autogen_task1_sh","status":"SUCCEEDED"},{"id":"autogen_task1_sf","status":"SUCCEEDED"},{"id":"autogen_task1_taun","status":"SUCCEEDED"},{"id":"autogen_task1_tauh","status":"SUCCEEDED"},{"id":"autogen_task1_lambda","status":"SUCCEEDED"},{"id":"autogen_task1_kc","status":"SUCCEEDED"},{"id":"autogen_task1_ks","status":"SUCCEEDED"},{"id":"autogen_task1_ff","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_phik","status":"SUCCEEDED"},{"id":"autogen_task1_phia","status":"SUCCEEDED"},{"id":"autogen_task1_phih","status":"SUCCEEDED"},{"id":"autogen_task1_phif","status":"SUCCEEDED"},{"id":"autogen_task1_phical","status":"SUCCEEDED"},{"id":"autogen_task1_cinf","status":"SUCCEEDED"},{"id":"autogen_task1_ica","status":"SUCCEEDED"},{"id":"autogen_task1_isk","status":"SUCCEEDED"},{"id":"autogen_task1_ibk","status":"SUCCEEDED"},{"id":"autogen_task1_ikdr","status":"SUCCEEDED"},{"id":"autogen_task1_ia","status":"SUCCEEDED"},{"id":"autogen_task1_ik","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_h","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_0000004","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.368468,"curves":[{"id":"autogen_curve_task1_c","status":"SUCCEEDED"}]}]}]}