{"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    449      0 --:--:-- --:--:-- --:--:--   451\n\r100  147k  100  147k    0     0   322k      0 --:--:-- --:--:-- --:--:--  322k\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 (14.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/rawLog.txt\nCompleted 2.4 KiB/2.4 KiB (29.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/BIOMD0000000367_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000367_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 32%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 80.8 KiB/80.8 KiB (560.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/outputs/reports.h5\nCompleted 2.6 KiB/81.6 KiB (22.0 KiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/rawLog.txt\nCompleted 2.6 KiB/81.6 KiB (22.0 KiB/s) with 3 file(s) remaining\rCompleted 11.7 KiB/81.6 KiB (79.6 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000367_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/outputs/BIOMD0000000367_url.sedml/autogen_plot_for_task1.pdf\nCompleted 11.7 KiB/81.6 KiB (79.6 KiB/s) with 2 file(s) remaining\rCompleted 75.5 KiB/81.6 KiB (455.6 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/output.zip\nCompleted 75.5 KiB/81.6 KiB (455.6 KiB/s) with 1 file(s) remaining\rCompleted 81.6 KiB/81.6 KiB (442.6 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000367-biopax2.owl  \n  inflating: contents/BIOMD0000000367-biopax3.owl  \n  inflating: contents/BIOMD0000000367-matlab.m  \n  inflating: contents/BIOMD0000000367-octave.m  \n  inflating: contents/BIOMD0000000367.m  \n  inflating: contents/BIOMD0000000367.ode  \n  inflating: contents/BIOMD0000000367.pdf  \n  inflating: contents/BIOMD0000000367.png  \n  inflating: contents/BIOMD0000000367.sci  \n  inflating: contents/BIOMD0000000367.svg  \n  inflating: contents/BIOMD0000000367_url.sedml  \n  inflating: contents/BIOMD0000000367_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 3.7 KiB/209.2 KiB (53.1 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000367-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367-biopax2.owl\nCompleted 3.7 KiB/209.2 KiB (53.1 KiB/s) with 15 file(s) remaining\rCompleted 8.0 KiB/209.2 KiB (52.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000367.png to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367.png\nCompleted 8.0 KiB/209.2 KiB (52.2 KiB/s) with 14 file(s) remaining\rCompleted 11.5 KiB/209.2 KiB (72.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000367-matlab.m to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367-matlab.m\nCompleted 11.5 KiB/209.2 KiB (72.8 KiB/s) with 13 file(s) remaining\rCompleted 11.7 KiB/209.2 KiB (63.4 KiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/curation_notes.txt\nCompleted 11.7 KiB/209.2 KiB (63.4 KiB/s) with 12 file(s) remaining\rCompleted 19.5 KiB/209.2 KiB (102.4 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000367_url.sedml to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367_url.sedml\nCompleted 19.5 KiB/209.2 KiB (102.4 KiB/s) with 11 file(s) remaining\rCompleted 20.3 KiB/209.2 KiB (103.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000367.svg to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367.svg\nCompleted 20.3 KiB/209.2 KiB (103.4 KiB/s) with 10 file(s) remaining\rCompleted 23.8 KiB/209.2 KiB (110.3 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000367-octave.m to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367-octave.m\nCompleted 23.8 KiB/209.2 KiB (110.3 KiB/s) with 9 file(s) remaining\rCompleted 62.2 KiB/209.2 KiB (285.8 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/curation_image.png\nCompleted 62.2 KiB/209.2 KiB (285.8 KiB/s) with 8 file(s) remaining\rCompleted 68.8 KiB/209.2 KiB (307.8 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000367_url.xml to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367_url.xml\nCompleted 68.8 KiB/209.2 KiB (307.8 KiB/s) with 7 file(s) remaining\rCompleted 70.7 KiB/209.2 KiB (312.5 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/manifest.xml\nCompleted 70.7 KiB/209.2 KiB (312.5 KiB/s) with 6 file(s) remaining\rCompleted 73.1 KiB/209.2 KiB (289.8 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/metadata.rdf\nCompleted 73.1 KiB/209.2 KiB (289.8 KiB/s) with 5 file(s) remaining\rCompleted 76.6 KiB/209.2 KiB (300.0 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000367.m to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367.m\nCompleted 76.6 KiB/209.2 KiB (300.0 KiB/s) with 4 file(s) remaining\rCompleted 80.7 KiB/209.2 KiB (305.8 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000367-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367-biopax3.owl\nCompleted 80.7 KiB/209.2 KiB (305.8 KiB/s) with 3 file(s) remaining\rCompleted 82.0 KiB/209.2 KiB (301.9 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000367.sci to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367.sci\nCompleted 82.0 KiB/209.2 KiB (301.9 KiB/s) with 2 file(s) remaining\rCompleted 207.6 KiB/209.2 KiB (741.8 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000367.pdf to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367.pdf\nCompleted 207.6 KiB/209.2 KiB (741.8 KiB/s) with 1 file(s) remaining\rCompleted 209.2 KiB/209.2 KiB (700.7 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000367.ode to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/contents/BIOMD0000000367.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (82.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1677b6669655060cc6/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000367_url.sedml\ncreating dataset /BIOMD0000000367_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-31aec891-e6493e8a-2fd2-950a40-cb8174, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000367_url.sedml/autogen_report_for_task1, shape: (13, 1001), type: float64\ndataset created, uuid: d-31aec891-e6493e8a-62c8-64978b-caa172, chunk_size: (13, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000367_url.sedml\ncreating attribute uri in /BIOMD0000000367_url.sedml\ncreating attribute _type in /BIOMD0000000367_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000367_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000367_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000367_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000367_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000367_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000367_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000367_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000367_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000367_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000367_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000367_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000367_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000367_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000367_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000367_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000367_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000367_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000367_url.sedml\ncreate_links: /BIOMD0000000367_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000367_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000367_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000367_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000367_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000367_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000367_url.sedml/autogen_report_for_task1, shape: (13, 1001), type: float64\niterating over chunks for /BIOMD0000000367_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000367_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b1677b6669655060cc6\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.\nProcess and upload the outputs of the simulation run ... 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.131028,"sedDocuments":[{"location":"BIOMD0000000367_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  BIOMD0000000367_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 13 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000367_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":0.75117,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.107503,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.147481,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_y","status":"SUCCEEDED"},{"id":"autogen_task1_z","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_mu_x","status":"SUCCEEDED"},{"id":"autogen_task1_zeta","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_mu_z","status":"SUCCEEDED"},{"id":"autogen_task1_epsilon","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_mu_z_star","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.399478,"curves":[{"id":"autogen_curve_task1_x","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_z","status":"SUCCEEDED"}]}]}]}