{"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    426      0 --:--:-- --:--:-- --:--:--   427\n\r100  217k  100  217k    0     0   486k      0 --:--:-- --:--:-- --:--:--  486k\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 (26.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/rawLog.txt\nCompleted 3.7 KiB/3.7 KiB (51.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/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/BIOMD0000000325_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000325_url.sedml/autogen_plot_for_task1.pdf (deflated 35%)\n  adding: outputs/reports.h5 (deflated 16%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 172.4 KiB/172.4 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/outputs/reports.h5\nCompleted 152.6 KiB/169.5 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/output.zip\nCompleted 152.6 KiB/169.5 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 158.1 KiB/169.5 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/outputs/plots.zip\nCompleted 158.1 KiB/169.5 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 166.9 KiB/169.5 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000325_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/outputs/BIOMD0000000325_url.sedml/autogen_plot_for_task1.pdf\nCompleted 166.9 KiB/169.5 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 169.5 KiB/169.5 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000325-biopax2.owl  \n  inflating: contents/BIOMD0000000325-biopax3.owl  \n  inflating: contents/BIOMD0000000325-matlab.m  \n  inflating: contents/BIOMD0000000325-octave.m  \n  inflating: contents/BIOMD0000000325.m  \n  inflating: contents/BIOMD0000000325.ode  \n  inflating: contents/BIOMD0000000325.pdf  \n  inflating: contents/BIOMD0000000325.png  \n  inflating: contents/BIOMD0000000325.sci  \n  inflating: contents/BIOMD0000000325.svg  \n  inflating: contents/BIOMD0000000325.vcml  \n  inflating: contents/BIOMD0000000325_url.sedml  \n  inflating: contents/BIOMD0000000325_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 23.4 KiB/~405.4 KiB (350.2 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000325-biopax3.owl to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325-biopax3.owl\nCompleted 23.4 KiB/~405.4 KiB (350.2 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 28.6 KiB/411.9 KiB (235.5 KiB/s) with 16 file(s) remaining                   \rupload: contents/BIOMD0000000325-matlab.m to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325-matlab.m\nCompleted 28.6 KiB/411.9 KiB (235.5 KiB/s) with 15 file(s) remaining\rCompleted 52.7 KiB/411.9 KiB (416.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000325_url.xml to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325_url.xml\nCompleted 52.7 KiB/411.9 KiB (416.7 KiB/s) with 14 file(s) remaining\rCompleted 57.9 KiB/411.9 KiB (437.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000325-octave.m to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325-octave.m\nCompleted 57.9 KiB/411.9 KiB (437.1 KiB/s) with 13 file(s) remaining\rCompleted 60.2 KiB/411.9 KiB (450.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000325.sci to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325.sci\nCompleted 60.2 KiB/411.9 KiB (450.1 KiB/s) with 12 file(s) remaining\rCompleted 96.1 KiB/411.9 KiB (677.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000325.vcml to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325.vcml\nCompleted 96.1 KiB/411.9 KiB (677.1 KiB/s) with 11 file(s) remaining\rCompleted 112.7 KiB/411.9 KiB (777.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000325-biopax2.owl to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325-biopax2.owl\nCompleted 112.7 KiB/411.9 KiB (777.4 KiB/s) with 10 file(s) remaining\rCompleted 133.6 KiB/411.9 KiB (914.1 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000325.svg to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325.svg\nCompleted 133.6 KiB/411.9 KiB (914.1 KiB/s) with 9 file(s) remaining\rCompleted 151.8 KiB/411.9 KiB (896.3 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000325_url.sedml to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325_url.sedml\nCompleted 151.8 KiB/411.9 KiB (896.3 KiB/s) with 8 file(s) remaining\rCompleted 152.2 KiB/411.9 KiB (860.3 KiB/s) with 8 file(s) remaining\rCompleted 177.7 KiB/411.9 KiB (995.5 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/curation_image.png\nCompleted 177.7 KiB/411.9 KiB (995.5 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/curation_notes.txt\nCompleted 177.7 KiB/411.9 KiB (995.5 KiB/s) with 6 file(s) remaining\rCompleted 179.6 KiB/411.9 KiB (942.7 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/manifest.xml\nCompleted 179.6 KiB/411.9 KiB (942.7 KiB/s) with 5 file(s) remaining\rCompleted 182.6 KiB/411.9 KiB (906.1 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000325.ode to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325.ode\nCompleted 182.6 KiB/411.9 KiB (906.1 KiB/s) with 4 file(s) remaining\rCompleted 187.8 KiB/411.9 KiB (918.7 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000325.m to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325.m\nCompleted 187.8 KiB/411.9 KiB (918.7 KiB/s) with 3 file(s) remaining\rCompleted 229.1 KiB/411.9 KiB (1.0 MiB/s) with 3 file(s) remaining  \rupload: contents/BIOMD0000000325.png to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325.png\nCompleted 229.1 KiB/411.9 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 233.3 KiB/411.9 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/metadata.rdf\nCompleted 233.3 KiB/411.9 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 411.9 KiB/411.9 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000325.pdf to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/contents/BIOMD0000000325.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (136.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710b320dcacb55678bad21/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000325_url.sedml\ncreating dataset /BIOMD0000000325_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-54ca4a34-844ad0ef-0181-9b5a32-2c3ab1, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000325_url.sedml/autogen_report_for_task1, shape: (33, 1001), type: float64\ndataset created, uuid: d-54ca4a34-844ad0ef-847b-8dd8bb-07b1a1, chunk_size: (33, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000325_url.sedml\ncreating attribute uri in /BIOMD0000000325_url.sedml\ncreating attribute _type in /BIOMD0000000325_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000325_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000325_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000325_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000325_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000325_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000325_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000325_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000325_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000325_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000325_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000325_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000325_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000325_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000325_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000325_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000325_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000325_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000325_url.sedml\ncreate_links: /BIOMD0000000325_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000325_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000325_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000325_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000325_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000325_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000325_url.sedml/autogen_report_for_task1, shape: (33, 1001), type: float64\niterating over chunks for /BIOMD0000000325_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 33, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000325_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710b320dcacb55678bad21\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 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.\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 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":18.467223,"sedDocuments":[{"location":"BIOMD0000000325_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  BIOMD0000000325_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 33 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000325_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":18.152264,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":17.249476,"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":0.327433,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_L","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_BR","status":"SUCCEEDED"},{"id":"autogen_task1_Rs","status":"SUCCEEDED"},{"id":"autogen_task1_KD","status":"SUCCEEDED"},{"id":"autogen_task1_kdegR","status":"SUCCEEDED"},{"id":"autogen_task1_kon","status":"SUCCEEDED"},{"id":"autogen_task1_koff","status":"SUCCEEDED"},{"id":"autogen_task1_kdegC","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_kdegX","status":"SUCCEEDED"},{"id":"autogen_task1_kdegA","status":"SUCCEEDED"},{"id":"autogen_task1_BI","status":"SUCCEEDED"},{"id":"autogen_task1_TFs","status":"SUCCEEDED"},{"id":"autogen_task1_kdegI","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_R_expression","status":"SUCCEEDED"},{"id":"autogen_task1_R_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_R_L_binding","status":"SUCCEEDED"},{"id":"autogen_task1_C_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_C_I_binding","status":"SUCCEEDED"},{"id":"autogen_task1_I_activation","status":"SUCCEEDED"},{"id":"autogen_task1_X_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_A_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_I_expression","status":"SUCCEEDED"},{"id":"autogen_task1_I_degradation","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.271646,"curves":[{"id":"autogen_curve_task1_L","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"}]}]}]}