{"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    436      0 --:--:-- --:--:-- --:--:--   437\n\r100  177k  100  177k    0     0   410k      0 --:--:-- --:--:-- --:--:--  410k\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 (24.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (48.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/BIOMD0000000402_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000402_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 22%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 101.4 KiB/101.4 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/outputs/reports.h5\nCompleted 88.2 KiB/107.7 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/output.zip\nCompleted 88.2 KiB/107.7 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 98.3 KiB/107.7 KiB (873.0 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000402_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/outputs/BIOMD0000000402_url.sedml/autogen_plot_for_task1.pdf\nCompleted 98.3 KiB/107.7 KiB (873.0 KiB/s) with 2 file(s) remaining\rCompleted 105.1 KiB/107.7 KiB (909.2 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/outputs/plots.zip\nCompleted 105.1 KiB/107.7 KiB (909.2 KiB/s) with 1 file(s) remaining\rCompleted 107.7 KiB/107.7 KiB (757.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000402-biopax2.owl  \n  inflating: contents/BIOMD0000000402-biopax3.owl  \n  inflating: contents/BIOMD0000000402-matlab.m  \n  inflating: contents/BIOMD0000000402-octave.m  \n  inflating: contents/BIOMD0000000402.m  \n  inflating: contents/BIOMD0000000402.ode  \n  inflating: contents/BIOMD0000000402.pdf  \n  inflating: contents/BIOMD0000000402.png  \n  inflating: contents/BIOMD0000000402.svg  \n  inflating: contents/BIOMD0000000402_url.sedml  \n  inflating: contents/BIOMD0000000402_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 6.2 KiB/270.0 KiB (70.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000402-biopax2.owl to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402-biopax2.owl\nCompleted 6.2 KiB/270.0 KiB (70.9 KiB/s) with 14 file(s) remaining\rCompleted 11.6 KiB/270.0 KiB (105.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000402-octave.m to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402-octave.m\nCompleted 11.6 KiB/270.0 KiB (105.9 KiB/s) with 13 file(s) remaining\rCompleted 17.0 KiB/270.0 KiB (144.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000402-matlab.m to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402-matlab.m\nCompleted 17.0 KiB/270.0 KiB (144.5 KiB/s) with 12 file(s) remaining\rCompleted 22.0 KiB/270.0 KiB (173.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000402.png to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402.png\nCompleted 22.0 KiB/270.0 KiB (173.1 KiB/s) with 11 file(s) remaining\rCompleted 36.7 KiB/270.0 KiB (271.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000402_url.sedml to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402_url.sedml\nCompleted 36.7 KiB/270.0 KiB (271.0 KiB/s) with 10 file(s) remaining\rCompleted 56.6 KiB/270.0 KiB (400.0 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000402_url.xml to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402_url.xml\nCompleted 56.6 KiB/270.0 KiB (400.0 KiB/s) with 9 file(s) remaining\rCompleted 57.5 KiB/270.0 KiB (401.7 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000402.svg to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402.svg\nCompleted 57.5 KiB/270.0 KiB (401.7 KiB/s) with 8 file(s) remaining\rCompleted 61.5 KiB/270.0 KiB (419.1 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/metadata.rdf\nCompleted 61.5 KiB/270.0 KiB (419.1 KiB/s) with 7 file(s) remaining\rCompleted 63.3 KiB/270.0 KiB (398.0 KiB/s) with 7 file(s) remaining\rCompleted 111.0 KiB/270.0 KiB (691.2 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/curation_image.png\nCompleted 111.0 KiB/270.0 KiB (691.2 KiB/s) with 6 file(s) remaining\rCompleted 111.5 KiB/270.0 KiB (682.1 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/curation_notes.txt\nCompleted 111.5 KiB/270.0 KiB (682.1 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/manifest.xml\nCompleted 111.5 KiB/270.0 KiB (682.1 KiB/s) with 4 file(s) remaining\rCompleted 118.2 KiB/270.0 KiB (636.9 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000402-biopax3.owl to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402-biopax3.owl\nCompleted 118.2 KiB/270.0 KiB (636.9 KiB/s) with 3 file(s) remaining\rCompleted 261.3 KiB/270.0 KiB (1.4 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000402.pdf to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402.pdf\nCompleted 261.3 KiB/270.0 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 266.7 KiB/270.0 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000402.m to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402.m\nCompleted 266.7 KiB/270.0 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 270.0 KiB/270.0 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000402.ode to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/contents/BIOMD0000000402.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (116.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c309a62a8be53f7d4e5/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000402_url.sedml\ncreating dataset /BIOMD0000000402_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-96b02bae-7de89bc9-7912-1df469-07b73f, chunk_size: (5, 1001)\ncreating dataset /BIOMD0000000402_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\ndataset created, uuid: d-96b02bae-7de89bc9-c961-a9f61f-9384e2, chunk_size: (27, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000402_url.sedml\ncreating attribute uri in /BIOMD0000000402_url.sedml\ncreating attribute _type in /BIOMD0000000402_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000402_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000402_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000402_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000402_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000402_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000402_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000402_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000402_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000402_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000402_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000402_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000402_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000402_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000402_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000402_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000402_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000402_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000402_url.sedml\ncreate_links: /BIOMD0000000402_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000402_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000402_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\niterating over chunks for /BIOMD0000000402_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000402_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000402_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000402_url.sedml/autogen_report_for_task1, shape: (27, 1001), type: float64\niterating over chunks for /BIOMD0000000402_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000402_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710c309a62a8be53f7d4e5\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 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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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":29.26553,"sedDocuments":[{"location":"BIOMD0000000402_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  BIOMD0000000402_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 27 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000402_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":28.915063,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":28.357391,"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":0.204021,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_z","status":"SUCCEEDED"},{"id":"autogen_task1_Tumour","status":"SUCCEEDED"},{"id":"autogen_task1_y1","status":"SUCCEEDED"},{"id":"autogen_task1_y2","status":"SUCCEEDED"},{"id":"autogen_task1_C_bar","status":"SUCCEEDED"},{"id":"autogen_task1_B_bar","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_beta1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha2","status":"SUCCEEDED"},{"id":"autogen_task1_beta2","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_g11","status":"SUCCEEDED"},{"id":"autogen_task1_g21","status":"SUCCEEDED"},{"id":"autogen_task1_g12","status":"SUCCEEDED"},{"id":"autogen_task1_g22","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_gammaT","status":"SUCCEEDED"},{"id":"autogen_task1_LT","status":"SUCCEEDED"},{"id":"autogen_task1_r11","status":"SUCCEEDED"},{"id":"autogen_task1_r21","status":"SUCCEEDED"},{"id":"autogen_task1_r12","status":"SUCCEEDED"},{"id":"autogen_task1_r22","status":"SUCCEEDED"},{"id":"autogen_task1_Compartment","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.235156,"curves":[{"id":"autogen_curve_task1_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_B","status":"SUCCEEDED"},{"id":"autogen_curve_task1_z","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Tumour","status":"SUCCEEDED"}]}]}]}