{"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    456      0 --:--:-- --:--:-- --:--:--   457\n\r100 89216  100 89216    0     0   197k      0 --:--:-- --:--:-- --:--:--  197k\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 (24.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/rawLog.txt\nCompleted 3.4 KiB/3.4 KiB (46.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 77%)\n  adding: outputs/Gerard2013.sedml/ (stored 0%)\n  adding: outputs/Gerard2013.sedml/plot_1_task1.pdf (deflated 25%)\n  adding: outputs/reports.h5 (deflated 65%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 40.0 KiB/40.0 KiB (453.5 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/outputs/reports.h5\nCompleted 29.3 KiB/61.7 KiB (368.2 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/output.zip\nCompleted 29.3 KiB/61.7 KiB (368.2 KiB/s) with 3 file(s) remaining\rCompleted 41.9 KiB/61.7 KiB (367.9 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/outputs/plots.zip\nCompleted 41.9 KiB/61.7 KiB (367.9 KiB/s) with 2 file(s) remaining\rCompleted 59.1 KiB/61.7 KiB (504.6 KiB/s) with 2 file(s) remaining\rupload: outputs/Gerard2013.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/outputs/Gerard2013.sedml/plot_1_task1.pdf\nCompleted 59.1 KiB/61.7 KiB (504.6 KiB/s) with 1 file(s) remaining\rCompleted 61.7 KiB/61.7 KiB (497.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Gerard2013-biopax2.owl  \n  inflating: contents/Gerard2013-biopax3.owl  \n  inflating: contents/Gerard2013-matlab.m  \n  inflating: contents/Gerard2013-octave.m  \n  inflating: contents/Gerard2013.cps  \n  inflating: contents/Gerard2013.ode  \n  inflating: contents/Gerard2013.sedml  \n  inflating: contents/Gerard2013.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 17.7 KiB/269.3 KiB (225.0 KiB/s) with 12 file(s) remaining\rupload: contents/Gerard2013-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/Gerard2013-biopax3.owl\nCompleted 17.7 KiB/269.3 KiB (225.0 KiB/s) with 11 file(s) remaining\rCompleted 23.9 KiB/269.3 KiB (238.5 KiB/s) with 11 file(s) remaining\rupload: contents/Gerard2013-matlab.m to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/Gerard2013-matlab.m\nCompleted 23.9 KiB/269.3 KiB (238.5 KiB/s) with 10 file(s) remaining\rCompleted 36.8 KiB/269.3 KiB (306.2 KiB/s) with 10 file(s) remaining\rupload: contents/Gerard2013-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/Gerard2013-biopax2.owl\nCompleted 36.8 KiB/269.3 KiB (306.2 KiB/s) with 9 file(s) remaining\rCompleted 43.1 KiB/269.3 KiB (347.9 KiB/s) with 9 file(s) remaining\rupload: contents/Gerard2013-octave.m to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/Gerard2013-octave.m\nCompleted 43.1 KiB/269.3 KiB (347.9 KiB/s) with 8 file(s) remaining\rCompleted 43.2 KiB/269.3 KiB (326.1 KiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/curation_notes.txt\nCompleted 43.2 KiB/269.3 KiB (326.1 KiB/s) with 7 file(s) remaining\rCompleted 60.3 KiB/269.3 KiB (420.4 KiB/s) with 7 file(s) remaining\rupload: contents/Gerard2013.sedml to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/Gerard2013.sedml\nCompleted 60.3 KiB/269.3 KiB (420.4 KiB/s) with 6 file(s) remaining\rCompleted 122.9 KiB/269.3 KiB (803.5 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/curation_image.png\nCompleted 122.9 KiB/269.3 KiB (803.5 KiB/s) with 5 file(s) remaining\rCompleted 124.3 KiB/269.3 KiB (788.5 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/manifest.xml\nCompleted 124.3 KiB/269.3 KiB (788.5 KiB/s) with 4 file(s) remaining\rCompleted 127.9 KiB/269.3 KiB (779.2 KiB/s) with 4 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/metadata.rdf\nCompleted 127.9 KiB/269.3 KiB (779.2 KiB/s) with 3 file(s) remaining\rCompleted 176.0 KiB/269.3 KiB (1020.1 KiB/s) with 3 file(s) remaining\rupload: contents/Gerard2013.xml to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/Gerard2013.xml\nCompleted 176.0 KiB/269.3 KiB (1020.1 KiB/s) with 2 file(s) remaining\rCompleted 180.6 KiB/269.3 KiB (1021.2 KiB/s) with 2 file(s) remaining\rupload: contents/Gerard2013.ode to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/Gerard2013.ode\nCompleted 180.6 KiB/269.3 KiB (1021.2 KiB/s) with 1 file(s) remaining\rCompleted 269.3 KiB/269.3 KiB (1.4 MiB/s) with 1 file(s) remaining   \rupload: contents/Gerard2013.cps to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/contents/Gerard2013.cps\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.4 KiB/7.4 KiB (104.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b8a195afd5df175f3e3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Gerard2013.sedml\ncreating dataset /Gerard2013.sedml/autogen_report_for_task1, shape: (27, 101), type: float64\ndataset created, uuid: d-562b6c6a-7e7cf67a-2aca-aba3d9-51e13f, chunk_size: (27, 101)\ncreating dataset /Gerard2013.sedml/plot_1_task1, shape: (5, 101), type: float64\ndataset created, uuid: d-562b6c6a-7e7cf67a-a91f-61fd7d-a20f56, chunk_size: (5, 101)\ncreating attribute combineArchiveLocation in /Gerard2013.sedml\ncreating attribute uri in /Gerard2013.sedml\ncreating attribute _type in /Gerard2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Gerard2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Gerard2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Gerard2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Gerard2013.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Gerard2013.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Gerard2013.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Gerard2013.sedml/autogen_report_for_task1\ncreating attribute uri in /Gerard2013.sedml/autogen_report_for_task1\ncreating attribute _type in /Gerard2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Gerard2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Gerard2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Gerard2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Gerard2013.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Gerard2013.sedml/plot_1_task1\ncreating attribute sedmlId in /Gerard2013.sedml/plot_1_task1\ncreating attribute sedmlName in /Gerard2013.sedml/plot_1_task1\ncreating attribute uri in /Gerard2013.sedml/plot_1_task1\ncreate_links: /\ngot link: Gerard2013.sedml\ncreate_links: /Gerard2013.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Gerard2013.sedml/autogen_report_for_task1 to tgt: /Gerard2013.sedml/autogen_report_for_task1, shape: (27, 101), type: float64\niterating over chunks for /Gerard2013.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 101, 1))\ndone with dataload for /Gerard2013.sedml/autogen_report_for_task1\nwrite_dataset src: /Gerard2013.sedml/plot_1_task1 to tgt: /Gerard2013.sedml/plot_1_task1, shape: (5, 101), type: float64\niterating over chunks for /Gerard2013.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 101, 1))\ndone with dataload for /Gerard2013.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b8a195afd5df175f3e3\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.\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.\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":20.505219,"sedDocuments":[{"location":"Gerard2013.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  Gerard2013.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      plot_1_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: Gerard2013.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_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: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":20.185537,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":19.597782,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.384574,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"},{"id":"p1_curve_4_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.076232,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Cdk","status":"SUCCEEDED"},{"id":"autogen_task1_Anaphase_promoting_complex_Phosphorylated","status":"SUCCEEDED"},{"id":"autogen_task1_Securin","status":"SUCCEEDED"},{"id":"autogen_task1_Anaphase_promoting_complex","status":"SUCCEEDED"},{"id":"autogen_task1_Anaphase_promoting_complex_total","status":"SUCCEEDED"},{"id":"autogen_task1_V_scdk","status":"SUCCEEDED"},{"id":"autogen_task1_k_d1cdk","status":"SUCCEEDED"},{"id":"autogen_task1_k_dcdk","status":"SUCCEEDED"},{"id":"autogen_task1_K_dcdk","status":"SUCCEEDED"},{"id":"autogen_task1_K_dsec","status":"SUCCEEDED"},{"id":"autogen_task1_k_2APC","status":"SUCCEEDED"},{"id":"autogen_task1_K_2APC","status":"SUCCEEDED"},{"id":"autogen_task1_V_1APC","status":"SUCCEEDED"},{"id":"autogen_task1_K_1APC","status":"SUCCEEDED"},{"id":"autogen_task1_V_ssec","status":"SUCCEEDED"},{"id":"autogen_task1_k_d1sec","status":"SUCCEEDED"},{"id":"autogen_task1_k_dsec","status":"SUCCEEDED"},{"id":"autogen_task1_nuclear","status":"SUCCEEDED"},{"id":"autogen_task1_Synthesis_Cdk","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_Cdk","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_Cdk_mediated_by_APC_P","status":"SUCCEEDED"},{"id":"autogen_task1_Phosphorylation_of_APC","status":"SUCCEEDED"},{"id":"autogen_task1_Dephosphorylation_of_APC","status":"SUCCEEDED"},{"id":"autogen_task1_Synthesis_of_Securin","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_Sec","status":"SUCCEEDED"},{"id":"autogen_task1_Degradation_of_Sec_mediated_by_APC_P","status":"SUCCEEDED"}]}]}]}