{"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    435      0 --:--:-- --:--:-- --:--:--   434\n\r100  151k  100  151k    0     0   322k      0 --:--:-- --:--:-- --:--:--  322k\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 (22.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/rawLog.txt\nCompleted 3.8 KiB/3.8 KiB (57.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/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/Bakshi2020 truncated minimal model.sedml/ (stored 0%)\n  adding: outputs/Bakshi2020 truncated minimal model.sedml/plot_1_task1.pdf (deflated 27%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 179.7 KiB/179.7 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/outputs/reports.h5\nCompleted 165.4 KiB/192.1 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/output.zip\nCompleted 165.4 KiB/192.1 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 175.4 KiB/192.1 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/outputs/plots.zip\nCompleted 175.4 KiB/192.1 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 189.4 KiB/192.1 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: outputs/Bakshi2020 truncated minimal model.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/outputs/Bakshi2020 truncated minimal model.sedml/plot_1_task1.pdf\nCompleted 189.4 KiB/192.1 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 192.1 KiB/192.1 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Bakshi2020 truncated minimal model-biopax2.owl  \n  inflating: contents/Bakshi2020 truncated minimal model-biopax3.owl  \n  inflating: contents/Bakshi2020 truncated minimal model-matlab.m  \n  inflating: contents/Bakshi2020 truncated minimal model.cps  \n  inflating: contents/Bakshi2020 truncated minimal model.ode  \n  inflating: contents/Bakshi2020 truncated minimal model.sedml  \n  inflating: contents/Bakshi2020 truncated minimal model.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 25.0 KiB/329.4 KiB (353.5 KiB/s) with 11 file(s) remaining\rupload: contents/Bakshi2020 truncated minimal model-biopax3.owl to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/Bakshi2020 truncated minimal model-biopax3.owl\nCompleted 25.0 KiB/329.4 KiB (353.5 KiB/s) with 10 file(s) remaining\rCompleted 42.0 KiB/329.4 KiB (323.6 KiB/s) with 10 file(s) remaining\rupload: contents/Bakshi2020 truncated minimal model-biopax2.owl to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/Bakshi2020 truncated minimal model-biopax2.owl\nCompleted 42.0 KiB/329.4 KiB (323.6 KiB/s) with 9 file(s) remaining\rCompleted 88.0 KiB/329.4 KiB (651.5 KiB/s) with 9 file(s) remaining\rupload: contents/Bakshi2020 truncated minimal model.xml to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/Bakshi2020 truncated minimal model.xml\nCompleted 88.0 KiB/329.4 KiB (651.5 KiB/s) with 8 file(s) remaining\rCompleted 91.2 KiB/329.4 KiB (653.8 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/metadata.rdf\nCompleted 91.2 KiB/329.4 KiB (653.8 KiB/s) with 7 file(s) remaining\rCompleted 97.0 KiB/329.4 KiB (682.8 KiB/s) with 7 file(s) remaining\rupload: contents/Bakshi2020 truncated minimal model-matlab.m to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/Bakshi2020 truncated minimal model-matlab.m\nCompleted 97.0 KiB/329.4 KiB (682.8 KiB/s) with 6 file(s) remaining\rCompleted 101.0 KiB/329.4 KiB (644.4 KiB/s) with 6 file(s) remaining\rupload: contents/Bakshi2020 truncated minimal model.ode to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/Bakshi2020 truncated minimal model.ode\nCompleted 101.0 KiB/329.4 KiB (644.4 KiB/s) with 5 file(s) remaining\rCompleted 179.5 KiB/329.4 KiB (1.1 MiB/s) with 5 file(s) remaining  \rupload: contents/Bakshi2020 truncated minimal model.cps to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/Bakshi2020 truncated minimal model.cps\nCompleted 179.5 KiB/329.4 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 308.6 KiB/329.4 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/curation_image.png\nCompleted 308.6 KiB/329.4 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 310.0 KiB/329.4 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/manifest.xml\nCompleted 310.0 KiB/329.4 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 310.1 KiB/329.4 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/curation_notes.txt\nCompleted 310.1 KiB/329.4 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 329.4 KiB/329.4 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/Bakshi2020 truncated minimal model.sedml to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/contents/Bakshi2020 truncated minimal model.sedml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.7 KiB/7.7 KiB (121.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a30f277b6669655054bc9/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Bakshi2020 truncated minimal model.sedml\ncreating dataset /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1, shape: (33, 1001), type: float64\ndataset created, uuid: d-f4789e2a-0983dea7-739e-3598bb-ec07b2, chunk_size: (33, 1001)\ncreating dataset /Bakshi2020 truncated minimal model.sedml/plot_1_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-f4789e2a-0983dea7-7e99-6b3cb8-67de0c, chunk_size: (7, 1001)\ncreating attribute combineArchiveLocation in /Bakshi2020 truncated minimal model.sedml\ncreating attribute uri in /Bakshi2020 truncated minimal model.sedml\ncreating attribute _type in /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\ncreating attribute uri in /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\ncreating attribute _type in /Bakshi2020 truncated minimal model.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Bakshi2020 truncated minimal model.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Bakshi2020 truncated minimal model.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Bakshi2020 truncated minimal model.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Bakshi2020 truncated minimal model.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Bakshi2020 truncated minimal model.sedml/plot_1_task1\ncreating attribute sedmlId in /Bakshi2020 truncated minimal model.sedml/plot_1_task1\ncreating attribute sedmlName in /Bakshi2020 truncated minimal model.sedml/plot_1_task1\ncreating attribute uri in /Bakshi2020 truncated minimal model.sedml/plot_1_task1\ncreate_links: /\ngot link: Bakshi2020 truncated minimal model.sedml\ncreate_links: /Bakshi2020 truncated minimal model.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1 to tgt: /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1, shape: (33, 1001), type: float64\niterating over chunks for /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 33, 1), slice(0, 1001, 1))\ndone with dataload for /Bakshi2020 truncated minimal model.sedml/autogen_report_for_task1\nwrite_dataset src: /Bakshi2020 truncated minimal model.sedml/plot_1_task1 to tgt: /Bakshi2020 truncated minimal model.sedml/plot_1_task1, shape: (7, 1001), type: float64\niterating over chunks for /Bakshi2020 truncated minimal model.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /Bakshi2020 truncated minimal model.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a30f277b6669655054bc9\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":17.34378,"sedDocuments":[{"location":"Bakshi2020 truncated minimal model.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  Bakshi2020 truncated minimal model.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      plot_1_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: Bakshi2020 truncated minimal model.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":17.04575,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":16.387892,"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":0.25987,"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":"p1_curve_5_task1","status":"SUCCEEDED"},{"id":"p1_curve_6_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.26289,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_C3","status":"SUCCEEDED"},{"id":"autogen_task1_C3b","status":"SUCCEEDED"},{"id":"autogen_task1_C3bB_closed","status":"SUCCEEDED"},{"id":"autogen_task1_C3bB_open","status":"SUCCEEDED"},{"id":"autogen_task1_C3bBb","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_B","status":"SUCCEEDED"},{"id":"autogen_task1_Bb","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_D","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_k5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k8","status":"SUCCEEDED"},{"id":"autogen_task1_k9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_ks1","status":"SUCCEEDED"},{"id":"autogen_task1_ks2","status":"SUCCEEDED"},{"id":"autogen_task1_d1","status":"SUCCEEDED"},{"id":"autogen_task1_d2","status":"SUCCEEDED"},{"id":"autogen_task1_Fluid_phase","status":"SUCCEEDED"},{"id":"autogen_task1_C3_hydrolysis","status":"SUCCEEDED"},{"id":"autogen_task1_C3bB_formation","status":"SUCCEEDED"},{"id":"autogen_task1_C3bB_conformational_change","status":"SUCCEEDED"},{"id":"autogen_task1_C3_convertase_formation","status":"SUCCEEDED"},{"id":"autogen_task1_C3_convertase_decay","status":"SUCCEEDED"},{"id":"autogen_task1_C3_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_C3_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_B_synthesis","status":"SUCCEEDED"},{"id":"autogen_task1_Factor_B_degradation","status":"SUCCEEDED"}]}]}]}