{"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  240k  100  240k    0     0   557k      0 --:--:-- --:--:-- --:--:--  557k\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 (14.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (24.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/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/BIOMD0000000004_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000004_url.sedml/autogen_plot_for_task1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 14%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 155.3 KiB/155.3 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/outputs/reports.h5\nCompleted 141.5 KiB/158.1 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/output.zip\nCompleted 141.5 KiB/158.1 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 144.1 KiB/158.1 KiB (982.4 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/rawLog.txt\nCompleted 144.1 KiB/158.1 KiB (982.4 KiB/s) with 2 file(s) remaining\rCompleted 149.6 KiB/158.1 KiB (787.2 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/outputs/plots.zip\nCompleted 149.6 KiB/158.1 KiB (787.2 KiB/s) with 1 file(s) remaining\rCompleted 158.1 KiB/158.1 KiB (769.5 KiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000004_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/outputs/BIOMD0000000004_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/BIOMD0000000004-biopax2.owl  \n  inflating: contents/BIOMD0000000004-biopax3.owl  \n  inflating: contents/BIOMD0000000004-matlab.m  \n  inflating: contents/BIOMD0000000004-octave.m  \n  inflating: contents/BIOMD0000000004.m  \n  inflating: contents/BIOMD0000000004.ode  \n  inflating: contents/BIOMD0000000004.pdf  \n  inflating: contents/BIOMD0000000004.png  \n  inflating: contents/BIOMD0000000004.sci  \n  inflating: contents/BIOMD0000000004.svg  \n  inflating: contents/BIOMD0000000004.vcml  \n  inflating: contents/BIOMD0000000004_manual.png  \n  inflating: contents/BIOMD0000000004_manual.svg  \n  inflating: contents/BIOMD0000000004_url.sedml  \n  inflating: contents/BIOMD0000000004_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 18.7 KiB/418.2 KiB (160.1 KiB/s) with 19 file(s) remaining\rupload: contents/BIOMD0000000004-biopax3.owl to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004-biopax3.owl\nCompleted 18.7 KiB/418.2 KiB (160.1 KiB/s) with 18 file(s) remaining\rCompleted 23.9 KiB/418.2 KiB (176.5 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000004-octave.m to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004-octave.m\nCompleted 23.9 KiB/418.2 KiB (176.5 KiB/s) with 17 file(s) remaining\rCompleted 26.7 KiB/418.2 KiB (192.3 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000004.sci to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004.sci\nCompleted 26.7 KiB/418.2 KiB (192.3 KiB/s) with 16 file(s) remaining\rCompleted 40.5 KiB/418.2 KiB (283.8 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000004-biopax2.owl to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004-biopax2.owl\nCompleted 40.5 KiB/418.2 KiB (283.8 KiB/s) with 15 file(s) remaining\rCompleted 45.7 KiB/418.2 KiB (266.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000004-matlab.m to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004-matlab.m\nCompleted 45.7 KiB/418.2 KiB (266.3 KiB/s) with 14 file(s) remaining\rCompleted 207.1 KiB/418.2 KiB (1.2 MiB/s) with 14 file(s) remaining \rupload: contents/BIOMD0000000004.pdf to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004.pdf\nCompleted 207.1 KiB/418.2 KiB (1.2 MiB/s) with 13 file(s) remaining\rCompleted 247.6 KiB/418.2 KiB (1.3 MiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000004.png to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004.png\nCompleted 247.6 KiB/418.2 KiB (1.3 MiB/s) with 12 file(s) remaining\rCompleted 258.7 KiB/418.2 KiB (1.3 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000004_url.sedml to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004_url.sedml\nCompleted 258.7 KiB/418.2 KiB (1.3 MiB/s) with 11 file(s) remaining\rCompleted 261.7 KiB/418.2 KiB (1.3 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000004.ode to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004.ode\nCompleted 261.7 KiB/418.2 KiB (1.3 MiB/s) with 10 file(s) remaining\rCompleted 275.5 KiB/418.2 KiB (1.3 MiB/s) with 10 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/curation_image.png\nCompleted 275.5 KiB/418.2 KiB (1.3 MiB/s) with 9 file(s) remaining\rCompleted 296.3 KiB/418.2 KiB (1.3 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000004_manual.svg to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004_manual.svg\nCompleted 296.3 KiB/418.2 KiB (1.3 MiB/s) with 8 file(s) remaining\rCompleted 315.9 KiB/418.2 KiB (1.4 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000004_url.xml to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004_url.xml\nCompleted 315.9 KiB/418.2 KiB (1.4 MiB/s) with 7 file(s) remaining\rCompleted 318.1 KiB/418.2 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/manifest.xml\nCompleted 318.1 KiB/418.2 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 318.2 KiB/418.2 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/curation_notes.txt\nCompleted 318.2 KiB/418.2 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 323.4 KiB/418.2 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000004.m to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004.m\nCompleted 323.4 KiB/418.2 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 363.9 KiB/418.2 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000004_manual.png to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004_manual.png\nCompleted 363.9 KiB/418.2 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 391.8 KiB/418.2 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000004.vcml to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004.vcml\nCompleted 391.8 KiB/418.2 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 397.3 KiB/418.2 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/metadata.rdf\nCompleted 397.3 KiB/418.2 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 418.2 KiB/418.2 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000004.svg to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/contents/BIOMD0000000004.svg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.8 KiB/9.8 KiB (97.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106fa0dcacb55678b3606/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000004_url.sedml\ncreating dataset /BIOMD0000000004_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-48180370-dcc57e9c-7800-866a28-ab68cc, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000004_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-48180370-dcc57e9c-e08c-010e24-cda225, chunk_size: (19, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000004_url.sedml\ncreating attribute uri in /BIOMD0000000004_url.sedml\ncreating attribute _type in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000004_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000004_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000004_url.sedml\ncreate_links: /BIOMD0000000004_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000004_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000004_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000004_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000004_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000004_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000004_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000004_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000004_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647106fa0dcacb55678b3606\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 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 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":20.260091,"sedDocuments":[{"location":"BIOMD0000000004_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  BIOMD0000000004_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: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000004_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":19.964396,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":19.367655,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.192871,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_MI","status":"SUCCEEDED"},{"id":"autogen_task1_XI","status":"SUCCEEDED"},{"id":"autogen_task1_V1","status":"SUCCEEDED"},{"id":"autogen_task1_V3","status":"SUCCEEDED"},{"id":"autogen_task1_VM1","status":"SUCCEEDED"},{"id":"autogen_task1_VM3","status":"SUCCEEDED"},{"id":"autogen_task1_Kc","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_reaction1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction7","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.287523,"curves":[{"id":"autogen_curve_task1_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_M","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_XI","status":"SUCCEEDED"}]}]}]}