{"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    446      0 --:--:-- --:--:-- --:--:--   446\n\r 37  134k   37 52046    0     0   120k      0  0:00:01 --:--:--  0:00:01  120k\r100  134k  100  134k    0     0   316k      0 --:--:-- --:--:-- --:--:-- 16.4M\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 (24.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/rawLog.txt\nCompleted 2.3 KiB/2.3 KiB (35.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/BIOMD0000000550_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000550_url.sedml/autogen_plot_for_task1.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 69%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 35.1 KiB/35.1 KiB (486.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/outputs/reports.h5\nCompleted 18.9 KiB/35.6 KiB (243.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/output.zip\nCompleted 18.9 KiB/35.6 KiB (243.6 KiB/s) with 3 file(s) remaining\rCompleted 24.4 KiB/35.6 KiB (245.6 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/outputs/plots.zip\nCompleted 24.4 KiB/35.6 KiB (245.6 KiB/s) with 2 file(s) remaining\rCompleted 27.1 KiB/35.6 KiB (224.6 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/rawLog.txt\nCompleted 27.1 KiB/35.6 KiB (224.6 KiB/s) with 1 file(s) remaining\rCompleted 35.6 KiB/35.6 KiB (247.2 KiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000550_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/outputs/BIOMD0000000550_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/BIOMD0000000550-biopax2.owl  \n  inflating: contents/BIOMD0000000550-biopax3.owl  \n  inflating: contents/BIOMD0000000550-matlab.m  \n  inflating: contents/BIOMD0000000550-octave.m  \n  inflating: contents/BIOMD0000000550.m  \n  inflating: contents/BIOMD0000000550.ode  \n  inflating: contents/BIOMD0000000550.pdf  \n  inflating: contents/BIOMD0000000550.png  \n  inflating: contents/BIOMD0000000550.svg  \n  inflating: contents/BIOMD0000000550_url.sedml  \n  inflating: contents/BIOMD0000000550_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 5.8 KiB/205.8 KiB (72.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000550-biopax3.owl to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550-biopax3.owl\nCompleted 5.8 KiB/205.8 KiB (72.7 KiB/s) with 14 file(s) remaining\rCompleted 8.9 KiB/205.8 KiB (81.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000550-matlab.m to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550-matlab.m\nCompleted 8.9 KiB/205.8 KiB (81.3 KiB/s) with 13 file(s) remaining\rCompleted 14.1 KiB/205.8 KiB (102.0 KiB/s) with 13 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/metadata.rdf\nCompleted 14.1 KiB/205.8 KiB (102.0 KiB/s) with 12 file(s) remaining\rCompleted 17.2 KiB/205.8 KiB (123.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000550-octave.m to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550-octave.m\nCompleted 17.2 KiB/205.8 KiB (123.1 KiB/s) with 11 file(s) remaining\rCompleted 23.4 KiB/205.8 KiB (162.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000550_url.sedml to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550_url.sedml\nCompleted 23.4 KiB/205.8 KiB (162.3 KiB/s) with 10 file(s) remaining\rCompleted 24.2 KiB/205.8 KiB (166.1 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000550.svg to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550.svg\nCompleted 24.2 KiB/205.8 KiB (166.1 KiB/s) with 9 file(s) remaining\rCompleted 29.7 KiB/205.8 KiB (196.8 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000550-biopax2.owl to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550-biopax2.owl\nCompleted 29.7 KiB/205.8 KiB (196.8 KiB/s) with 8 file(s) remaining\rCompleted 48.0 KiB/205.8 KiB (289.9 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000550_url.xml to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550_url.xml\nCompleted 48.0 KiB/205.8 KiB (289.9 KiB/s) with 7 file(s) remaining\rCompleted 62.3 KiB/205.8 KiB (341.2 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/curation_image.png\nCompleted 62.3 KiB/205.8 KiB (341.2 KiB/s) with 6 file(s) remaining\rCompleted 62.6 KiB/205.8 KiB (336.8 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/curation_notes.txt\nCompleted 62.6 KiB/205.8 KiB (336.8 KiB/s) with 5 file(s) remaining\rCompleted 195.2 KiB/205.8 KiB (1.0 MiB/s) with 5 file(s) remaining \rupload: contents/BIOMD0000000550.pdf to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550.pdf\nCompleted 195.2 KiB/205.8 KiB (1.0 MiB/s) with 4 file(s) remaining\rCompleted 197.0 KiB/205.8 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/manifest.xml\nCompleted 197.0 KiB/205.8 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 200.1 KiB/205.8 KiB (982.6 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000550.m to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550.m\nCompleted 200.1 KiB/205.8 KiB (982.6 KiB/s) with 2 file(s) remaining\rCompleted 204.4 KiB/205.8 KiB (990.0 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000550.png to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550.png\nCompleted 204.4 KiB/205.8 KiB (990.0 KiB/s) with 1 file(s) remaining\rCompleted 205.8 KiB/205.8 KiB (962.6 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000550.ode to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/contents/BIOMD0000000550.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (112.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647111779a62a8be53f896da/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000550_url.sedml\ncreating dataset /BIOMD0000000550_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\ndataset created, uuid: d-1bbeb56a-5518908b-3ff9-cbffbd-1c151b, chunk_size: (3, 1001)\ncreating dataset /BIOMD0000000550_url.sedml/autogen_report_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-1bbeb56a-5518908b-ad6a-7c3c05-9d17c1, chunk_size: (9, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000550_url.sedml\ncreating attribute uri in /BIOMD0000000550_url.sedml\ncreating attribute _type in /BIOMD0000000550_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000550_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000550_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000550_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000550_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000550_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000550_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000550_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000550_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000550_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000550_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000550_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000550_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000550_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000550_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000550_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000550_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000550_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000550_url.sedml\ncreate_links: /BIOMD0000000550_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000550_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000550_url.sedml/autogen_plot_for_task1, shape: (3, 1001), type: float64\niterating over chunks for /BIOMD0000000550_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000550_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000550_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000550_url.sedml/autogen_report_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000550_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000550_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647111779a62a8be53f896da\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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.090072,"sedDocuments":[{"location":"BIOMD0000000550_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  BIOMD0000000550_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 9 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000550_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":0.715178,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.118984,"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":0.122503,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_task1_species_2","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_1","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_2","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_3","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_4","status":"SUCCEEDED"},{"id":"autogen_task1_parameter_5","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.374997,"curves":[{"id":"autogen_curve_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_2","status":"SUCCEEDED"}]}]}]}