{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    426      0 --:--:-- --:--:-- --:--:--   425\n\r100  211k  100  211k    0     0   469k      0 --:--:-- --:--:-- --:--:--  469k\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 (24.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/rawLog.txt\nCompleted 3.5 KiB/3.5 KiB (53.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/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/BIOMD0000000271_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000271_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 184.4 KiB/184.4 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/outputs/reports.h5\nCompleted 172.5 KiB/192.6 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/output.zip\nCompleted 172.5 KiB/192.6 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 182.8 KiB/192.6 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000271_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/outputs/BIOMD0000000271_url.sedml/autogen_plot_for_task1.pdf\nCompleted 182.8 KiB/192.6 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 185.5 KiB/192.6 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/rawLog.txt\nCompleted 185.5 KiB/192.6 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 192.6 KiB/192.6 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000271-biopax2.owl  \n  inflating: contents/BIOMD0000000271-biopax3.owl  \n  inflating: contents/BIOMD0000000271-matlab.m  \n  inflating: contents/BIOMD0000000271-octave.m  \n  inflating: contents/BIOMD0000000271.m  \n  inflating: contents/BIOMD0000000271.ode  \n  inflating: contents/BIOMD0000000271.pdf  \n  inflating: contents/BIOMD0000000271.png  \n  inflating: contents/BIOMD0000000271.svg  \n  inflating: contents/BIOMD0000000271_url.sedml  \n  inflating: contents/BIOMD0000000271_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 25.8 KiB/377.4 KiB (354.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000271-biopax3.owl to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271-biopax3.owl\nCompleted 25.8 KiB/377.4 KiB (354.5 KiB/s) with 14 file(s) remaining\rCompleted 30.7 KiB/377.4 KiB (251.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000271-octave.m to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271-octave.m\nCompleted 30.7 KiB/377.4 KiB (251.7 KiB/s) with 13 file(s) remaining\rCompleted 48.1 KiB/377.4 KiB (369.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000271.svg to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271.svg\nCompleted 48.1 KiB/377.4 KiB (369.5 KiB/s) with 12 file(s) remaining\rCompleted 49.9 KiB/377.4 KiB (373.0 KiB/s) with 12 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/manifest.xml\nCompleted 49.9 KiB/377.4 KiB (373.0 KiB/s) with 11 file(s) remaining\rCompleted 68.3 KiB/377.4 KiB (491.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000271-biopax2.owl to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271-biopax2.owl\nCompleted 68.3 KiB/377.4 KiB (491.4 KiB/s) with 10 file(s) remaining\rCompleted 73.2 KiB/377.4 KiB (514.9 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000271-matlab.m to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271-matlab.m\nCompleted 73.2 KiB/377.4 KiB (514.9 KiB/s) with 9 file(s) remaining\rCompleted 89.2 KiB/377.4 KiB (561.4 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000271_url.sedml to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271_url.sedml\nCompleted 89.2 KiB/377.4 KiB (561.4 KiB/s) with 8 file(s) remaining\rCompleted 115.4 KiB/377.4 KiB (704.2 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000271_url.xml to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271_url.xml\nCompleted 115.4 KiB/377.4 KiB (704.2 KiB/s) with 7 file(s) remaining\rCompleted 132.8 KiB/377.4 KiB (756.5 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/curation_image.png\nCompleted 132.8 KiB/377.4 KiB (756.5 KiB/s) with 6 file(s) remaining\rCompleted 132.9 KiB/377.4 KiB (721.2 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/curation_notes.txt\nCompleted 132.9 KiB/377.4 KiB (721.2 KiB/s) with 5 file(s) remaining\rCompleted 137.8 KiB/377.4 KiB (731.9 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000271.m to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271.m\nCompleted 137.8 KiB/377.4 KiB (731.9 KiB/s) with 4 file(s) remaining\rCompleted 147.3 KiB/377.4 KiB (761.2 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/metadata.rdf\nCompleted 147.3 KiB/377.4 KiB (761.2 KiB/s) with 3 file(s) remaining\rCompleted 187.9 KiB/377.4 KiB (945.1 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000271.png to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271.png\nCompleted 187.9 KiB/377.4 KiB (945.1 KiB/s) with 2 file(s) remaining\rCompleted 190.8 KiB/377.4 KiB (947.6 KiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000271.ode to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271.ode\nCompleted 190.8 KiB/377.4 KiB (947.6 KiB/s) with 1 file(s) remaining\rCompleted 377.4 KiB/377.4 KiB (1.8 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000271.pdf to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/contents/BIOMD0000000271.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (141.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a839a62a8be53f79f96/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000271_url.sedml\ncreating dataset /BIOMD0000000271_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-af0e8204-f45c4685-825f-911580-2b9479, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000271_url.sedml/autogen_report_for_task1, shape: (28, 1001), type: float64\ndataset created, uuid: d-af0e8204-f45c4685-7893-c644a3-d583b8, chunk_size: (28, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000271_url.sedml\ncreating attribute uri in /BIOMD0000000271_url.sedml\ncreating attribute _type in /BIOMD0000000271_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000271_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000271_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000271_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000271_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000271_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000271_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000271_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000271_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000271_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000271_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000271_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000271_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000271_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000271_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000271_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000271_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000271_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000271_url.sedml\ncreate_links: /BIOMD0000000271_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000271_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000271_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000271_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000271_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000271_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000271_url.sedml/autogen_report_for_task1, shape: (28, 1001), type: float64\niterating over chunks for /BIOMD0000000271_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 28, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000271_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710a839a62a8be53f79f96\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.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":18.952541,"sedDocuments":[{"location":"BIOMD0000000271_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  BIOMD0000000271_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 28 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000271_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":18.632339,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":17.779106,"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":0.254496,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_EpoR","status":"SUCCEEDED"},{"id":"autogen_task1_Epo","status":"SUCCEEDED"},{"id":"autogen_task1_Epo_EpoR","status":"SUCCEEDED"},{"id":"autogen_task1_Epo_EpoRi","status":"SUCCEEDED"},{"id":"autogen_task1_dEpoi","status":"SUCCEEDED"},{"id":"autogen_task1_dEpoe","status":"SUCCEEDED"},{"id":"autogen_task1_kt","status":"SUCCEEDED"},{"id":"autogen_task1_Bmax","status":"SUCCEEDED"},{"id":"autogen_task1_kon","status":"SUCCEEDED"},{"id":"autogen_task1_koff","status":"SUCCEEDED"},{"id":"autogen_task1_ke","status":"SUCCEEDED"},{"id":"autogen_task1_kex","status":"SUCCEEDED"},{"id":"autogen_task1_kdi","status":"SUCCEEDED"},{"id":"autogen_task1_kde","status":"SUCCEEDED"},{"id":"autogen_task1_Epo_medium","status":"SUCCEEDED"},{"id":"autogen_task1_Epo_cells","status":"SUCCEEDED"},{"id":"autogen_task1_medium","status":"SUCCEEDED"},{"id":"autogen_task1_cellsurface","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_7","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_8","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.464367,"curves":[{"id":"autogen_curve_task1_EpoR","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Epo","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Epo_EpoR","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Epo_EpoRi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_dEpoi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_dEpoe","status":"SUCCEEDED"}]}]}]}