{"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    425      0 --:--:-- --:--:-- --:--:--   425\n\r100  164k  100  164k    0     0   367k      0 --:--:-- --:--:-- --:--:--  367k\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 (26.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (48.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/BIOMD0000000157_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000157_url.sedml/autogen_plot_for_task1.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 21%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 102.5 KiB/102.5 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/outputs/reports.h5\nCompleted 91.7 KiB/113.6 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/output.zip\nCompleted 91.7 KiB/113.6 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 99.9 KiB/113.6 KiB (888.4 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/outputs/plots.zip\nCompleted 99.9 KiB/113.6 KiB (888.4 KiB/s) with 2 file(s) remaining\rCompleted 102.6 KiB/113.6 KiB (889.2 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/rawLog.txt\nCompleted 102.6 KiB/113.6 KiB (889.2 KiB/s) with 1 file(s) remaining\rCompleted 113.6 KiB/113.6 KiB (873.7 KiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000157_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/outputs/BIOMD0000000157_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/BIOMD0000000157-biopax2.owl  \n  inflating: contents/BIOMD0000000157-biopax3.owl  \n  inflating: contents/BIOMD0000000157-matlab.m  \n  inflating: contents/BIOMD0000000157-octave.m  \n  inflating: contents/BIOMD0000000157.m  \n  inflating: contents/BIOMD0000000157.ode  \n  inflating: contents/BIOMD0000000157.pdf  \n  inflating: contents/BIOMD0000000157.png  \n  inflating: contents/BIOMD0000000157.sci  \n  inflating: contents/BIOMD0000000157.svg  \n  inflating: contents/BIOMD0000000157_url.sedml  \n  inflating: contents/BIOMD0000000157_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 11.0 KiB/~265.8 KiB (181.8 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000157-biopax2.owl to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157-biopax2.owl\nCompleted 11.0 KiB/~265.8 KiB (181.8 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 11.1 KiB/271.2 KiB (98.2 KiB/s) with 15 file(s) remaining                    \rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/curation_notes.txt\nCompleted 11.1 KiB/271.2 KiB (98.2 KiB/s) with 14 file(s) remaining\rCompleted 15.0 KiB/271.2 KiB (121.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000157-matlab.m to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157-matlab.m\nCompleted 15.0 KiB/271.2 KiB (121.2 KiB/s) with 13 file(s) remaining\rCompleted 25.4 KiB/271.2 KiB (187.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000157.svg to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157.svg\nCompleted 25.4 KiB/271.2 KiB (187.5 KiB/s) with 12 file(s) remaining\rCompleted 45.1 KiB/271.2 KiB (329.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000157.png to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157.png\nCompleted 45.1 KiB/271.2 KiB (329.0 KiB/s) with 11 file(s) remaining\rCompleted 49.1 KiB/271.2 KiB (353.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000157-octave.m to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157-octave.m\nCompleted 49.1 KiB/271.2 KiB (353.4 KiB/s) with 10 file(s) remaining\rCompleted 59.8 KiB/271.2 KiB (387.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000157_url.sedml to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157_url.sedml\nCompleted 59.8 KiB/271.2 KiB (387.8 KiB/s) with 9 file(s) remaining\rCompleted 61.3 KiB/271.2 KiB (367.9 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000157.sci to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157.sci\nCompleted 61.3 KiB/271.2 KiB (367.9 KiB/s) with 8 file(s) remaining\rCompleted 64.9 KiB/271.2 KiB (376.7 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/metadata.rdf\nCompleted 64.9 KiB/271.2 KiB (376.7 KiB/s) with 7 file(s) remaining\rCompleted 87.8 KiB/271.2 KiB (492.4 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/curation_image.jpeg\nCompleted 87.8 KiB/271.2 KiB (492.4 KiB/s) with 6 file(s) remaining\rCompleted 89.7 KiB/271.2 KiB (460.5 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/manifest.xml\nCompleted 89.7 KiB/271.2 KiB (460.5 KiB/s) with 5 file(s) remaining\rCompleted 91.8 KiB/271.2 KiB (463.7 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000157.ode to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157.ode\nCompleted 91.8 KiB/271.2 KiB (463.7 KiB/s) with 4 file(s) remaining\rCompleted 105.2 KiB/271.2 KiB (523.9 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000157_url.xml to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157_url.xml\nCompleted 105.2 KiB/271.2 KiB (523.9 KiB/s) with 3 file(s) remaining\rCompleted 119.4 KiB/271.2 KiB (586.1 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000157-biopax3.owl to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157-biopax3.owl\nCompleted 119.4 KiB/271.2 KiB (586.1 KiB/s) with 2 file(s) remaining\rCompleted 123.4 KiB/271.2 KiB (594.0 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000157.m to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157.m\nCompleted 123.4 KiB/271.2 KiB (594.0 KiB/s) with 1 file(s) remaining\rCompleted 271.2 KiB/271.2 KiB (1.2 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000157.pdf to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/contents/BIOMD0000000157.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (130.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647108f79a62a8be53f77003/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000157_url.sedml\ncreating dataset /BIOMD0000000157_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-877b4963-92cb292d-bd25-4a5844-1b7496, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000157_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-877b4963-92cb292d-dbee-1bae00-9598b6, chunk_size: (19, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000157_url.sedml\ncreating attribute uri in /BIOMD0000000157_url.sedml\ncreating attribute _type in /BIOMD0000000157_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000157_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000157_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000157_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000157_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000157_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000157_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000157_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000157_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000157_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000157_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000157_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000157_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000157_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000157_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000157_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000157_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000157_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000157_url.sedml\ncreate_links: /BIOMD0000000157_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000157_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000157_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000157_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000157_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000157_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000157_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000157_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000157_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647108f79a62a8be53f77003\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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.401329,"sedDocuments":[{"location":"BIOMD0000000157_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  BIOMD0000000157_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 19 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000157_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":0.932714,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.200901,"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":0.187706,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_y","status":"SUCCEEDED"},{"id":"autogen_task1_y0","status":"SUCCEEDED"},{"id":"autogen_task1_beta_x","status":"SUCCEEDED"},{"id":"autogen_task1_psi","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_x","status":"SUCCEEDED"},{"id":"autogen_task1_beta_y","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_y","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_0","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_alpha_k","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"},{"id":"autogen_task1_R5","status":"SUCCEEDED"},{"id":"autogen_task1_R6","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.42656,"curves":[{"id":"autogen_curve_task1_x","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y0","status":"SUCCEEDED"}]}]}]}