{"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    442      0 --:--:-- --:--:-- --:--:--   444\n\r100  270k  100  270k    0     0   632k      0 --:--:-- --:--:-- --:--:--  632k\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 (25.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/rawLog.txt\nCompleted 3.5 KiB/3.5 KiB (49.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/BIOMD0000000296_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000296_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 146.6 KiB/146.6 KiB (864.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/outputs/reports.h5\nCompleted 136.0 KiB/159.8 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/output.zip\nCompleted 136.0 KiB/159.8 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 144.6 KiB/159.8 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/outputs/plots.zip\nCompleted 144.6 KiB/159.8 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 157.1 KiB/159.8 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000296_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/outputs/BIOMD0000000296_url.sedml/autogen_plot_for_task1.pdf\nCompleted 157.1 KiB/159.8 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 159.8 KiB/159.8 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000296-biopax2.owl  \n  inflating: contents/BIOMD0000000296-biopax3.owl  \n  inflating: contents/BIOMD0000000296-matlab.m  \n  inflating: contents/BIOMD0000000296-octave.m  \n  inflating: contents/BIOMD0000000296.m  \n  inflating: contents/BIOMD0000000296.ode  \n  inflating: contents/BIOMD0000000296.pdf  \n  inflating: contents/BIOMD0000000296.png  \n  inflating: contents/BIOMD0000000296.sci  \n  inflating: contents/BIOMD0000000296.svg  \n  inflating: contents/BIOMD0000000296.vcml  \n  inflating: contents/BIOMD0000000296_url.sedml  \n  inflating: contents/BIOMD0000000296_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 15.2 KiB/459.9 KiB (224.9 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000296-biopax2.owl to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296-biopax2.owl\nCompleted 15.2 KiB/459.9 KiB (224.9 KiB/s) with 16 file(s) remaining\rCompleted 20.2 KiB/459.9 KiB (172.7 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000296-matlab.m to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296-matlab.m\nCompleted 20.2 KiB/459.9 KiB (172.7 KiB/s) with 15 file(s) remaining\rCompleted 25.2 KiB/459.9 KiB (206.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000296-octave.m to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296-octave.m\nCompleted 25.2 KiB/459.9 KiB (206.1 KiB/s) with 14 file(s) remaining\rCompleted 87.8 KiB/459.9 KiB (643.5 KiB/s) with 14 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/curation_image.png\nCompleted 87.8 KiB/459.9 KiB (643.5 KiB/s) with 13 file(s) remaining\rCompleted 148.0 KiB/459.9 KiB (1.0 MiB/s) with 13 file(s) remaining \rupload: contents/BIOMD0000000296.png to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296.png\nCompleted 148.0 KiB/459.9 KiB (1.0 MiB/s) with 12 file(s) remaining\rCompleted 153.0 KiB/459.9 KiB (988.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000296.m to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296.m\nCompleted 153.0 KiB/459.9 KiB (988.5 KiB/s) with 11 file(s) remaining\rCompleted 156.0 KiB/459.9 KiB (975.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000296.ode to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296.ode\nCompleted 156.0 KiB/459.9 KiB (975.5 KiB/s) with 10 file(s) remaining\rCompleted 171.9 KiB/459.9 KiB (1.0 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000296_url.sedml to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296_url.sedml\nCompleted 171.9 KiB/459.9 KiB (1.0 MiB/s) with 9 file(s) remaining\rCompleted 351.3 KiB/459.9 KiB (1.9 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000296.pdf to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296.pdf\nCompleted 351.3 KiB/459.9 KiB (1.9 MiB/s) with 8 file(s) remaining\rCompleted 378.1 KiB/459.9 KiB (2.0 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000296_url.xml to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296_url.xml\nCompleted 378.1 KiB/459.9 KiB (2.0 MiB/s) with 7 file(s) remaining\rCompleted 378.2 KiB/459.9 KiB (1.9 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/curation_notes.txt\nCompleted 378.2 KiB/459.9 KiB (1.9 MiB/s) with 6 file(s) remaining\rCompleted 380.1 KiB/459.9 KiB (1.8 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/manifest.xml\nCompleted 380.1 KiB/459.9 KiB (1.8 MiB/s) with 5 file(s) remaining\rCompleted 384.0 KiB/459.9 KiB (1.8 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/metadata.rdf\nCompleted 384.0 KiB/459.9 KiB (1.8 MiB/s) with 4 file(s) remaining\rCompleted 386.3 KiB/459.9 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000296.sci to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296.sci\nCompleted 386.3 KiB/459.9 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 419.5 KiB/459.9 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000296.vcml to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296.vcml\nCompleted 419.5 KiB/459.9 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 441.3 KiB/459.9 KiB (1.7 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000296-biopax3.owl to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296-biopax3.owl\nCompleted 441.3 KiB/459.9 KiB (1.7 MiB/s) with 1 file(s) remaining\rCompleted 459.9 KiB/459.9 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000296.svg to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/contents/BIOMD0000000296.svg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (127.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ad40dcacb55678ba312/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000296_url.sedml\ncreating dataset /BIOMD0000000296_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-85831780-ecca4903-f35a-d2e241-d70254, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000296_url.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\ndataset created, uuid: d-85831780-ecca4903-c3ce-532d5f-f979ea, chunk_size: (29, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000296_url.sedml\ncreating attribute uri in /BIOMD0000000296_url.sedml\ncreating attribute _type in /BIOMD0000000296_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000296_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000296_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000296_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000296_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000296_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000296_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000296_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000296_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000296_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000296_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000296_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000296_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000296_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000296_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000296_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000296_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000296_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000296_url.sedml\ncreate_links: /BIOMD0000000296_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000296_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000296_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000296_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000296_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000296_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000296_url.sedml/autogen_report_for_task1, shape: (29, 1001), type: float64\niterating over chunks for /BIOMD0000000296_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 29, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000296_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710ad40dcacb55678ba312\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 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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.500928,"sedDocuments":[{"location":"BIOMD0000000296_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  BIOMD0000000296_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 29 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000296_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":1.050662,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.170447,"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":0.260577,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_IPTG","status":"SUCCEEDED"},{"id":"autogen_task1_C1","status":"SUCCEEDED"},{"id":"autogen_task1_C2","status":"SUCCEEDED"},{"id":"autogen_task1_A1","status":"SUCCEEDED"},{"id":"autogen_task1_A2","status":"SUCCEEDED"},{"id":"autogen_task1_sink","status":"SUCCEEDED"},{"id":"autogen_task1_source","status":"SUCCEEDED"},{"id":"autogen_task1_kc1","status":"SUCCEEDED"},{"id":"autogen_task1_kc2","status":"SUCCEEDED"},{"id":"autogen_task1_Cm","status":"SUCCEEDED"},{"id":"autogen_task1_D","status":"SUCCEEDED"},{"id":"autogen_task1_kA1","status":"SUCCEEDED"},{"id":"autogen_task1_kA2","status":"SUCCEEDED"},{"id":"autogen_task1_d2","status":"SUCCEEDED"},{"id":"autogen_task1_K2","status":"SUCCEEDED"},{"id":"autogen_task1_d1","status":"SUCCEEDED"},{"id":"autogen_task1_K1","status":"SUCCEEDED"},{"id":"autogen_task1_dAA1","status":"SUCCEEDED"},{"id":"autogen_task1_dAA2","status":"SUCCEEDED"},{"id":"autogen_task1_environment","status":"SUCCEEDED"},{"id":"autogen_task1_J0","status":"SUCCEEDED"},{"id":"autogen_task1_J1","status":"SUCCEEDED"},{"id":"autogen_task1_J2","status":"SUCCEEDED"},{"id":"autogen_task1_J3","status":"SUCCEEDED"},{"id":"autogen_task1_J4","status":"SUCCEEDED"},{"id":"autogen_task1_J5","status":"SUCCEEDED"},{"id":"autogen_task1_J6","status":"SUCCEEDED"},{"id":"autogen_task1_J7","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.480641,"curves":[{"id":"autogen_curve_task1_IPTG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_sink","status":"SUCCEEDED"},{"id":"autogen_curve_task1_source","status":"SUCCEEDED"}]}]}]}