{"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    439      0 --:--:-- --:--:-- --:--:--   439\r100   139  100   139    0     0    437      0 --:--:-- --:--:-- --:--:--   437\n\r100  316k  100  316k    0     0   695k      0 --:--:-- --:--:-- --:--:--  695k\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 (19.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/rawLog.txt\nCompleted 4.5 KiB/4.5 KiB (63.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/reports.h5 (deflated 9%)\n  adding: outputs/BIOMD0000000021_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000021_url.sedml/autogen_plot_for_task1.pdf (deflated 26%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/311.2 KiB (5.7 MiB/s) with 1 file(s) remaining\rCompleted 311.2 KiB/311.2 KiB (3.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/outputs/reports.h5\nCompleted 256.0 KiB/317.2 KiB (5.7 MiB/s) with 4 file(s) remaining\rCompleted 293.6 KiB/317.2 KiB (3.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/output.zip\nCompleted 293.6 KiB/317.2 KiB (3.2 MiB/s) with 3 file(s) remaining\rCompleted 302.4 KiB/317.2 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/outputs/plots.zip\nCompleted 302.4 KiB/317.2 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 314.4 KiB/317.2 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000021_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/outputs/BIOMD0000000021_url.sedml/autogen_plot_for_task1.pdf\nCompleted 314.4 KiB/317.2 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 317.2 KiB/317.2 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000021-biopax2.owl  \n  inflating: contents/BIOMD0000000021-biopax3.owl  \n  inflating: contents/BIOMD0000000021-matlab.m  \n  inflating: contents/BIOMD0000000021-octave.m  \n  inflating: contents/BIOMD0000000021.m  \n  inflating: contents/BIOMD0000000021.ode  \n  inflating: contents/BIOMD0000000021.pdf  \n  inflating: contents/BIOMD0000000021.png  \n  inflating: contents/BIOMD0000000021.sci  \n  inflating: contents/BIOMD0000000021.svg  \n  inflating: contents/BIOMD0000000021.vcml  \n  inflating: contents/BIOMD0000000021_url.sedml  \n  inflating: contents/BIOMD0000000021_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 45.7 KiB/693.7 KiB (555.9 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000021-biopax3.owl to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021-biopax3.owl\nCompleted 45.7 KiB/693.7 KiB (555.9 KiB/s) with 16 file(s) remaining\rCompleted 58.3 KiB/693.7 KiB (568.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000021-matlab.m to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021-matlab.m\nCompleted 58.3 KiB/693.7 KiB (568.0 KiB/s) with 15 file(s) remaining\rCompleted 66.9 KiB/693.7 KiB (494.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000021.sci to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021.sci\nCompleted 66.9 KiB/693.7 KiB (494.5 KiB/s) with 14 file(s) remaining\rCompleted 96.5 KiB/693.7 KiB (702.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000021-biopax2.owl to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021-biopax2.owl\nCompleted 96.5 KiB/693.7 KiB (702.6 KiB/s) with 13 file(s) remaining\rCompleted 144.2 KiB/693.7 KiB (971.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000021.svg to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021.svg\nCompleted 144.2 KiB/693.7 KiB (971.5 KiB/s) with 12 file(s) remaining\rCompleted 164.9 KiB/693.7 KiB (1.0 MiB/s) with 12 file(s) remaining  \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/curation_image.png\nCompleted 164.9 KiB/693.7 KiB (1.0 MiB/s) with 11 file(s) remaining\rCompleted 177.5 KiB/693.7 KiB (1.1 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000021-octave.m to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021-octave.m\nCompleted 177.5 KiB/693.7 KiB (1.1 MiB/s) with 10 file(s) remaining\rCompleted 179.5 KiB/693.7 KiB (1.0 MiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/manifest.xml\nCompleted 179.5 KiB/693.7 KiB (1.0 MiB/s) with 9 file(s) remaining\rCompleted 244.2 KiB/693.7 KiB (1.4 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000021.vcml to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021.vcml\nCompleted 244.2 KiB/693.7 KiB (1.4 MiB/s) with 8 file(s) remaining\rCompleted 267.9 KiB/693.7 KiB (1.4 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000021_url.sedml to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021_url.sedml\nCompleted 267.9 KiB/693.7 KiB (1.4 MiB/s) with 7 file(s) remaining\rCompleted 267.9 KiB/693.7 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/curation_notes.txt\nCompleted 267.9 KiB/693.7 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 270.2 KiB/693.7 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/metadata.rdf\nCompleted 270.2 KiB/693.7 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 277.9 KiB/693.7 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000021.ode to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021.ode\nCompleted 277.9 KiB/693.7 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 504.8 KiB/693.7 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000021.pdf to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021.pdf\nCompleted 504.8 KiB/693.7 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 554.3 KiB/693.7 KiB (2.4 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000021_url.xml to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021_url.xml\nCompleted 554.3 KiB/693.7 KiB (2.4 MiB/s) with 2 file(s) remaining\rCompleted 567.0 KiB/693.7 KiB (2.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000021.m to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021.m\nCompleted 567.0 KiB/693.7 KiB (2.4 MiB/s) with 1 file(s) remaining\rCompleted 693.7 KiB/693.7 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000021.png to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/contents/BIOMD0000000021.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.3 KiB/9.3 KiB (151.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471073949c0d898ffdd9172/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000021_url.sedml\ncreating dataset /BIOMD0000000021_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\ndataset created, uuid: d-256123fa-c4f62556-6894-f74588-525de7, chunk_size: (11, 1001)\ncreating dataset /BIOMD0000000021_url.sedml/autogen_report_for_task1, shape: (41, 1001), type: float64\ndataset created, uuid: d-256123fa-c4f62556-a334-f25beb-ba1419, chunk_size: (41, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000021_url.sedml\ncreating attribute uri in /BIOMD0000000021_url.sedml\ncreating attribute _type in /BIOMD0000000021_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000021_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000021_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000021_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000021_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000021_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000021_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000021_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000021_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000021_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000021_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000021_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000021_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000021_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000021_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000021_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000021_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000021_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000021_url.sedml\ncreate_links: /BIOMD0000000021_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000021_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000021_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\niterating over chunks for /BIOMD0000000021_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000021_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000021_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000021_url.sedml/autogen_report_for_task1, shape: (41, 1001), type: float64\niterating over chunks for /BIOMD0000000021_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 41, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000021_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471073949c0d898ffdd9172\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.\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 and upload the outputs of the simulation run ... 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":20.727857,"sedDocuments":[{"location":"BIOMD0000000021_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  BIOMD0000000021_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 41 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 10 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000021_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":20.375727,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":19.494424,"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":0.353779,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_P0","status":"SUCCEEDED"},{"id":"autogen_task1_T0","status":"SUCCEEDED"},{"id":"autogen_task1_P1","status":"SUCCEEDED"},{"id":"autogen_task1_T1","status":"SUCCEEDED"},{"id":"autogen_task1_P2","status":"SUCCEEDED"},{"id":"autogen_task1_T2","status":"SUCCEEDED"},{"id":"autogen_task1_CC","status":"SUCCEEDED"},{"id":"autogen_task1_Cn","status":"SUCCEEDED"},{"id":"autogen_task1_Mp","status":"SUCCEEDED"},{"id":"autogen_task1_Mt","status":"SUCCEEDED"},{"id":"autogen_task1_Pt","status":"SUCCEEDED"},{"id":"autogen_task1_Tt","status":"SUCCEEDED"},{"id":"autogen_task1_V_mT","status":"SUCCEEDED"},{"id":"autogen_task1_V_dT","status":"SUCCEEDED"},{"id":"autogen_task1_Cell","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_0000002","status":"SUCCEEDED"},{"id":"autogen_task1_P0_to_P1","status":"SUCCEEDED"},{"id":"autogen_task1_T0_to_T1","status":"SUCCEEDED"},{"id":"autogen_task1_P1_to_P0","status":"SUCCEEDED"},{"id":"autogen_task1_T1_to_T0","status":"SUCCEEDED"},{"id":"autogen_task1_P1_to_P2","status":"SUCCEEDED"},{"id":"autogen_task1_T1_to_T2","status":"SUCCEEDED"},{"id":"autogen_task1_P2_to_P1","status":"SUCCEEDED"},{"id":"autogen_task1_T2_to_T1","status":"SUCCEEDED"},{"id":"autogen_task1_P0_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_T0_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_P1_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_T1_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_P2_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_T2_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_PT_complex_formation","status":"SUCCEEDED"},{"id":"autogen_task1_PT_complex_nucleation","status":"SUCCEEDED"},{"id":"autogen_task1_PT_complex_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_PTnucl_complex_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_production","status":"SUCCEEDED"},{"id":"autogen_task1_Mt_production","status":"SUCCEEDED"},{"id":"autogen_task1_P0_production","status":"SUCCEEDED"},{"id":"autogen_task1_T0_production","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_Mt_degradation","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.375977,"curves":[{"id":"autogen_curve_task1_P0","status":"SUCCEEDED"},{"id":"autogen_curve_task1_T0","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_T1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_T2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cn","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mt","status":"SUCCEEDED"}]}]}]}