{"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    442      0 --:--:-- --:--:-- --:--:--   442\n\r100  145k  100  145k    0     0   341k      0 --:--:-- --:--:-- --:--:--  341k\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 3 SED documents:\n  SED documents (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n  Tasks (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n  Outputs (6):\n    Succeeded: 6\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (23.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/rawLog.txt\nCompleted 11.3 KiB/11.3 KiB (169.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 90%)\n  adding: outputs/Saad2017.sedml/ (stored 0%)\n  adding: outputs/Saad2017.sedml/plot_1_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 61%)\n  adding: outputs/Saad2017-no treatment.sedml/ (stored 0%)\n  adding: outputs/Saad2017-no treatment.sedml/plot_1_task1.pdf (deflated 31%)\n  adding: outputs/Saad2017-no checkpoint.sedml/ (stored 0%)\n  adding: outputs/Saad2017-no checkpoint.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 106.0 KiB/106.0 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/outputs/reports.h5\nCompleted 63.2 KiB/111.8 KiB (789.3 KiB/s) with 6 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/output.zip\nCompleted 63.2 KiB/111.8 KiB (789.3 KiB/s) with 5 file(s) remaining\rCompleted 72.7 KiB/111.8 KiB (646.5 KiB/s) with 5 file(s) remaining\rupload: outputs/Saad2017.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/outputs/Saad2017.sedml/plot_1_task1.pdf\nCompleted 72.7 KiB/111.8 KiB (646.5 KiB/s) with 4 file(s) remaining\rCompleted 81.3 KiB/111.8 KiB (699.7 KiB/s) with 4 file(s) remaining\rupload: outputs/Saad2017-no checkpoint.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/outputs/Saad2017-no checkpoint.sedml/plot_1_task1.pdf\nCompleted 81.3 KiB/111.8 KiB (699.7 KiB/s) with 3 file(s) remaining\rCompleted 90.7 KiB/111.8 KiB (756.3 KiB/s) with 3 file(s) remaining\rupload: outputs/Saad2017-no treatment.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/outputs/Saad2017-no treatment.sedml/plot_1_task1.pdf\nCompleted 90.7 KiB/111.8 KiB (756.3 KiB/s) with 2 file(s) remaining\rCompleted 93.6 KiB/111.8 KiB (701.6 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/rawLog.txt\nCompleted 93.6 KiB/111.8 KiB (701.6 KiB/s) with 1 file(s) remaining\rCompleted 111.8 KiB/111.8 KiB (798.7 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Fig.1A.png     \n  inflating: contents/Fig.1B.png     \n  inflating: contents/Fig.2B.png     \n  inflating: contents/Fig.2C.png     \n  inflating: contents/Fig.2E.png     \n  inflating: contents/Fig.3.png      \n  inflating: contents/Saad2017-biopax2.owl  \n  inflating: contents/Saad2017-biopax3.owl  \n  inflating: contents/Saad2017-matlab.m  \n  inflating: contents/Saad2017-no checkpoint-biopax2.owl  \n  inflating: contents/Saad2017-no checkpoint-biopax3.owl  \n  inflating: contents/Saad2017-no checkpoint-matlab.m  \n  inflating: contents/Saad2017-no checkpoint-octave.m  \n  inflating: contents/Saad2017-no checkpoint.cps  \n  inflating: contents/Saad2017-no checkpoint.ode  \n  inflating: contents/Saad2017-no checkpoint.sedml  \n  inflating: contents/Saad2017-no checkpoint.xml  \n  inflating: contents/Saad2017-no treatment-biopax2.owl  \n  inflating: contents/Saad2017-no treatment-biopax3.owl  \n  inflating: contents/Saad2017-no treatment-matlab.m  \n  inflating: contents/Saad2017-no treatment-octave.m  \n  inflating: contents/Saad2017-no treatment.cps  \n  inflating: contents/Saad2017-no treatment.ode  \n  inflating: contents/Saad2017-no treatment.sedml  \n  inflating: contents/Saad2017-no treatment.xml  \n  inflating: contents/Saad2017-octave.m  \n  inflating: contents/Saad2017.cps   \n  inflating: contents/Saad2017.ode   \n  inflating: contents/Saad2017.sedml  \n  inflating: contents/Saad2017.xml   \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 13.8 KiB/708.7 KiB (185.3 KiB/s) with 34 file(s) remaining\rupload: contents/Fig.1A.png to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Fig.1A.png\nCompleted 13.8 KiB/708.7 KiB (185.3 KiB/s) with 33 file(s) remaining\rCompleted 24.5 KiB/708.7 KiB (199.6 KiB/s) with 33 file(s) remaining\rupload: contents/Fig.2B.png to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Fig.2B.png\nCompleted 24.5 KiB/708.7 KiB (199.6 KiB/s) with 32 file(s) remaining\rCompleted 30.1 KiB/708.7 KiB (235.3 KiB/s) with 32 file(s) remaining\rupload: contents/Saad2017-matlab.m to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-matlab.m\nCompleted 30.1 KiB/708.7 KiB (235.3 KiB/s) with 31 file(s) remaining\rCompleted 41.8 KiB/708.7 KiB (317.8 KiB/s) with 31 file(s) remaining\rupload: contents/Fig.2C.png to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Fig.2C.png\nCompleted 41.8 KiB/708.7 KiB (317.8 KiB/s) with 30 file(s) remaining\rCompleted 111.9 KiB/708.7 KiB (802.2 KiB/s) with 30 file(s) remaining\rupload: contents/Saad2017-no checkpoint.cps to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no checkpoint.cps\nCompleted 111.9 KiB/708.7 KiB (802.2 KiB/s) with 29 file(s) remaining\rCompleted 123.9 KiB/708.7 KiB (862.5 KiB/s) with 29 file(s) remaining\rupload: contents/Saad2017-no checkpoint-biopax2.owl to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no checkpoint-biopax2.owl\nCompleted 123.9 KiB/708.7 KiB (862.5 KiB/s) with 28 file(s) remaining\rCompleted 140.3 KiB/708.7 KiB (886.5 KiB/s) with 28 file(s) remaining\rupload: contents/Saad2017-no checkpoint-biopax3.owl to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no checkpoint-biopax3.owl\nCompleted 140.3 KiB/708.7 KiB (886.5 KiB/s) with 27 file(s) remaining\rCompleted 162.3 KiB/708.7 KiB (1005.0 KiB/s) with 27 file(s) remaining\rupload: contents/Saad2017-biopax3.owl to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-biopax3.owl\nCompleted 162.3 KiB/708.7 KiB (1005.0 KiB/s) with 26 file(s) remaining\rCompleted 167.2 KiB/708.7 KiB (988.6 KiB/s) with 26 file(s) remaining \rupload: contents/Saad2017-no checkpoint-matlab.m to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no checkpoint-matlab.m\nCompleted 167.2 KiB/708.7 KiB (988.6 KiB/s) with 25 file(s) remaining\rCompleted 172.2 KiB/708.7 KiB (1000.9 KiB/s) with 25 file(s) remaining\rupload: contents/Saad2017-no checkpoint-octave.m to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no checkpoint-octave.m\nCompleted 172.2 KiB/708.7 KiB (1000.9 KiB/s) with 24 file(s) remaining\rCompleted 175.3 KiB/708.7 KiB (993.5 KiB/s) with 24 file(s) remaining \rupload: contents/Saad2017-no checkpoint.ode to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no checkpoint.ode\nCompleted 175.3 KiB/708.7 KiB (993.5 KiB/s) with 23 file(s) remaining\rCompleted 189.6 KiB/708.7 KiB (1.0 MiB/s) with 23 file(s) remaining  \rupload: contents/Saad2017-no checkpoint.sedml to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no checkpoint.sedml\nCompleted 189.6 KiB/708.7 KiB (1.0 MiB/s) with 22 file(s) remaining\rCompleted 204.0 KiB/708.7 KiB (1.1 MiB/s) with 22 file(s) remaining\rupload: contents/Saad2017-no treatment-biopax2.owl to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no treatment-biopax2.owl\nCompleted 204.0 KiB/708.7 KiB (1.1 MiB/s) with 21 file(s) remaining\rCompleted 223.3 KiB/708.7 KiB (1.1 MiB/s) with 21 file(s) remaining\rupload: contents/Saad2017-no treatment-biopax3.owl to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no treatment-biopax3.owl\nCompleted 223.3 KiB/708.7 KiB (1.1 MiB/s) with 20 file(s) remaining\rCompleted 281.2 KiB/708.7 KiB (1.4 MiB/s) with 20 file(s) remaining\rupload: contents/Saad2017-no checkpoint.xml to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no checkpoint.xml\nCompleted 281.2 KiB/708.7 KiB (1.4 MiB/s) with 19 file(s) remaining\rCompleted 286.6 KiB/708.7 KiB (1.2 MiB/s) with 19 file(s) remaining\rupload: contents/Saad2017-no treatment-octave.m to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no treatment-octave.m\nCompleted 286.6 KiB/708.7 KiB (1.2 MiB/s) with 18 file(s) remaining\rCompleted 292.1 KiB/708.7 KiB (1.2 MiB/s) with 18 file(s) remaining\rupload: contents/Saad2017-no treatment-matlab.m to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no treatment-matlab.m\nCompleted 292.1 KiB/708.7 KiB (1.2 MiB/s) with 17 file(s) remaining\rCompleted 371.3 KiB/708.7 KiB (1.5 MiB/s) with 17 file(s) remaining\rupload: contents/Saad2017-no treatment.cps to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no treatment.cps\nCompleted 371.3 KiB/708.7 KiB (1.5 MiB/s) with 16 file(s) remaining\rCompleted 374.8 KiB/708.7 KiB (1.5 MiB/s) with 16 file(s) remaining\rupload: contents/Saad2017-no treatment.ode to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no treatment.ode\nCompleted 374.8 KiB/708.7 KiB (1.5 MiB/s) with 15 file(s) remaining\rCompleted 441.4 KiB/708.7 KiB (1.8 MiB/s) with 15 file(s) remaining\rupload: contents/Saad2017-no treatment.xml to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no treatment.xml\nCompleted 441.4 KiB/708.7 KiB (1.8 MiB/s) with 14 file(s) remaining\rCompleted 457.9 KiB/708.7 KiB (1.8 MiB/s) with 14 file(s) remaining\rupload: contents/Saad2017-no treatment.sedml to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-no treatment.sedml\nCompleted 457.9 KiB/708.7 KiB (1.8 MiB/s) with 13 file(s) remaining\rCompleted 461.7 KiB/708.7 KiB (1.8 MiB/s) with 13 file(s) remaining\rupload: contents/Saad2017.ode to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017.ode\nCompleted 461.7 KiB/708.7 KiB (1.8 MiB/s) with 12 file(s) remaining\rCompleted 467.3 KiB/708.7 KiB (1.8 MiB/s) with 12 file(s) remaining\rupload: contents/Saad2017-octave.m to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-octave.m\nCompleted 467.3 KiB/708.7 KiB (1.8 MiB/s) with 11 file(s) remaining\rCompleted 484.9 KiB/708.7 KiB (1.8 MiB/s) with 11 file(s) remaining\rupload: contents/Saad2017.sedml to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017.sedml\nCompleted 484.9 KiB/708.7 KiB (1.8 MiB/s) with 10 file(s) remaining\rCompleted 567.4 KiB/708.7 KiB (2.1 MiB/s) with 10 file(s) remaining\rupload: contents/Saad2017.cps to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017.cps\nCompleted 567.4 KiB/708.7 KiB (2.1 MiB/s) with 9 file(s) remaining\rCompleted 567.6 KiB/708.7 KiB (1.9 MiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/curation_notes.txt\nCompleted 567.6 KiB/708.7 KiB (1.9 MiB/s) with 8 file(s) remaining\rCompleted 572.1 KiB/708.7 KiB (1.9 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/metadata.rdf\nCompleted 572.1 KiB/708.7 KiB (1.9 MiB/s) with 7 file(s) remaining\rCompleted 583.1 KiB/708.7 KiB (1.9 MiB/s) with 7 file(s) remaining\rupload: contents/Fig.1B.png to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Fig.1B.png\nCompleted 583.1 KiB/708.7 KiB (1.9 MiB/s) with 6 file(s) remaining\rCompleted 598.6 KiB/708.7 KiB (1.9 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/curation_image.png\nCompleted 598.6 KiB/708.7 KiB (1.9 MiB/s) with 5 file(s) remaining\rCompleted 602.5 KiB/708.7 KiB (1.9 MiB/s) with 5 file(s) remaining\rCompleted 669.8 KiB/708.7 KiB (2.1 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/manifest.xml\nCompleted 669.8 KiB/708.7 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: contents/Saad2017.xml to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017.xml\nCompleted 669.8 KiB/708.7 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 686.3 KiB/708.7 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 697.9 KiB/708.7 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/Saad2017-biopax2.owl to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Saad2017-biopax2.owl\nCompleted 697.9 KiB/708.7 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: contents/Fig.2E.png to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Fig.2E.png\nCompleted 697.9 KiB/708.7 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 708.7 KiB/708.7 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: contents/Fig.3.png to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/contents/Fig.3.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 15.3 KiB/15.3 KiB (215.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f16e6262268786a361e0/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Saad2017-no checkpoint.sedml\ncreating dataset /Saad2017-no checkpoint.sedml/autogen_report_for_task1, shape: (23, 201), type: float64\ndataset created, uuid: d-10e79495-1c2eabf8-0030-9bf789-b96bd8, chunk_size: (23, 201)\ncreating dataset /Saad2017-no checkpoint.sedml/plot_1_task1, shape: (4, 201), type: float64\ndataset created, uuid: d-10e79495-1c2eabf8-c4d6-27cef8-eed570, chunk_size: (4, 201)\ncreating group /Saad2017-no treatment.sedml\ncreating dataset /Saad2017-no treatment.sedml/autogen_report_for_task1, shape: (27, 201), type: float64\ndataset created, uuid: d-10e79495-1c2eabf8-f75d-e42872-119c71, chunk_size: (27, 201)\ncreating dataset /Saad2017-no treatment.sedml/plot_1_task1, shape: (5, 201), type: float64\ndataset created, uuid: d-10e79495-1c2eabf8-cb7e-b9e076-9c6316, chunk_size: (5, 201)\ncreating group /Saad2017.sedml\ncreating dataset /Saad2017.sedml/autogen_report_for_task1, shape: (29, 201), type: float64\ndataset created, uuid: d-10e79495-1c2eabf8-87a2-35d4e9-6de4ce, chunk_size: (29, 201)\ncreating dataset /Saad2017.sedml/plot_1_task1, shape: (5, 201), type: float64\ndataset created, uuid: d-10e79495-1c2eabf8-5fea-b0ee0f-8e3c11, chunk_size: (5, 201)\ncreating attribute combineArchiveLocation in /Saad2017-no checkpoint.sedml\ncreating attribute uri in /Saad2017-no checkpoint.sedml\ncreating attribute _type in /Saad2017-no checkpoint.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Saad2017-no checkpoint.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Saad2017-no checkpoint.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Saad2017-no checkpoint.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Saad2017-no checkpoint.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Saad2017-no checkpoint.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Saad2017-no checkpoint.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Saad2017-no checkpoint.sedml/autogen_report_for_task1\ncreating attribute uri in /Saad2017-no checkpoint.sedml/autogen_report_for_task1\ncreating attribute _type in /Saad2017-no checkpoint.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Saad2017-no checkpoint.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Saad2017-no checkpoint.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Saad2017-no checkpoint.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Saad2017-no checkpoint.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Saad2017-no checkpoint.sedml/plot_1_task1\ncreating attribute sedmlId in /Saad2017-no checkpoint.sedml/plot_1_task1\ncreating attribute sedmlName in /Saad2017-no checkpoint.sedml/plot_1_task1\ncreating attribute uri in /Saad2017-no checkpoint.sedml/plot_1_task1\ncreating attribute combineArchiveLocation in /Saad2017-no treatment.sedml\ncreating attribute uri in /Saad2017-no treatment.sedml\ncreating attribute _type in /Saad2017-no treatment.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Saad2017-no treatment.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Saad2017-no treatment.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Saad2017-no treatment.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Saad2017-no treatment.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Saad2017-no treatment.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Saad2017-no treatment.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Saad2017-no treatment.sedml/autogen_report_for_task1\ncreating attribute uri in /Saad2017-no treatment.sedml/autogen_report_for_task1\ncreating attribute _type in /Saad2017-no treatment.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Saad2017-no treatment.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Saad2017-no treatment.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Saad2017-no treatment.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Saad2017-no treatment.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Saad2017-no treatment.sedml/plot_1_task1\ncreating attribute sedmlId in /Saad2017-no treatment.sedml/plot_1_task1\ncreating attribute sedmlName in /Saad2017-no treatment.sedml/plot_1_task1\ncreating attribute uri in /Saad2017-no treatment.sedml/plot_1_task1\ncreating attribute combineArchiveLocation in /Saad2017.sedml\ncreating attribute uri in /Saad2017.sedml\ncreating attribute _type in /Saad2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Saad2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Saad2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Saad2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Saad2017.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Saad2017.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Saad2017.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Saad2017.sedml/autogen_report_for_task1\ncreating attribute uri in /Saad2017.sedml/autogen_report_for_task1\ncreating attribute _type in /Saad2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Saad2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Saad2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Saad2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Saad2017.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Saad2017.sedml/plot_1_task1\ncreating attribute sedmlId in /Saad2017.sedml/plot_1_task1\ncreating attribute sedmlName in /Saad2017.sedml/plot_1_task1\ncreating attribute uri in /Saad2017.sedml/plot_1_task1\ncreate_links: /\ngot link: Saad2017-no checkpoint.sedml\ngot link: Saad2017-no treatment.sedml\ngot link: Saad2017.sedml\ncreate_links: /Saad2017-no checkpoint.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ncreate_links: /Saad2017-no treatment.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ncreate_links: /Saad2017.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Saad2017-no checkpoint.sedml/autogen_report_for_task1 to tgt: /Saad2017-no checkpoint.sedml/autogen_report_for_task1, shape: (23, 201), type: float64\niterating over chunks for /Saad2017-no checkpoint.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 23, 1), slice(0, 201, 1))\ndone with dataload for /Saad2017-no checkpoint.sedml/autogen_report_for_task1\nwrite_dataset src: /Saad2017-no checkpoint.sedml/plot_1_task1 to tgt: /Saad2017-no checkpoint.sedml/plot_1_task1, shape: (4, 201), type: float64\niterating over chunks for /Saad2017-no checkpoint.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 201, 1))\ndone with dataload for /Saad2017-no checkpoint.sedml/plot_1_task1\nwrite_dataset src: /Saad2017-no treatment.sedml/autogen_report_for_task1 to tgt: /Saad2017-no treatment.sedml/autogen_report_for_task1, shape: (27, 201), type: float64\niterating over chunks for /Saad2017-no treatment.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 27, 1), slice(0, 201, 1))\ndone with dataload for /Saad2017-no treatment.sedml/autogen_report_for_task1\nwrite_dataset src: /Saad2017-no treatment.sedml/plot_1_task1 to tgt: /Saad2017-no treatment.sedml/plot_1_task1, shape: (5, 201), type: float64\niterating over chunks for /Saad2017-no treatment.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 201, 1))\ndone with dataload for /Saad2017-no treatment.sedml/plot_1_task1\nwrite_dataset src: /Saad2017.sedml/autogen_report_for_task1 to tgt: /Saad2017.sedml/autogen_report_for_task1, shape: (29, 201), type: float64\niterating over chunks for /Saad2017.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 29, 1), slice(0, 201, 1))\ndone with dataload for /Saad2017.sedml/autogen_report_for_task1\nwrite_dataset src: /Saad2017.sedml/plot_1_task1 to tgt: /Saad2017.sedml/plot_1_task1, shape: (5, 201), type: float64\niterating over chunks for /Saad2017.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 201, 1))\ndone with dataload for /Saad2017.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f16e6262268786a361e0\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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":2.692201,"sedDocuments":[{"location":"Saad2017-no checkpoint.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 3 SED-ML documents with 3 models, 3 simulations, 3 tasks, 3 reports, and 3 plots:\r\n  Saad2017-no checkpoint.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 23 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n  Saad2017-no treatment.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  Saad2017.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 29 data sets\r\n    Plots (1):\r\n      plot_1_task1: 4 curves\r\n\r\nExecuting SED-ML file 1: Saad2017-no checkpoint.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":0.811985,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.21205,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.347452,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.078788,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_a1","status":"SUCCEEDED"},{"id":"autogen_task1_a2","status":"SUCCEEDED"},{"id":"autogen_task1_alpha2","status":"SUCCEEDED"},{"id":"autogen_task1_u1","status":"SUCCEEDED"},{"id":"autogen_task1_u2","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_alpha3","status":"SUCCEEDED"},{"id":"autogen_task1_bladder_cancer_tme","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_growth","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_killing","status":"SUCCEEDED"},{"id":"autogen_task1_effector_activation_by_cancer","status":"SUCCEEDED"},{"id":"autogen_task1_effector_activation_by_BCG","status":"SUCCEEDED"},{"id":"autogen_task1_effector_depletion_by_cancer","status":"SUCCEEDED"},{"id":"autogen_task1_effector_death","status":"SUCCEEDED"},{"id":"autogen_task1_BCG_source__therapy","status":"SUCCEEDED"},{"id":"autogen_task1_BCG_death","status":"SUCCEEDED"},{"id":"autogen_task1_BCG_killing_by_effector","status":"SUCCEEDED"}]}]},{"location":"Saad2017-no treatment.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 2 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 2\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 2: Saad2017-no treatment.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":0.576332,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.119055,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.176732,"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":0.086332,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_a1","status":"SUCCEEDED"},{"id":"autogen_task1_a2","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_alpha2","status":"SUCCEEDED"},{"id":"autogen_task1_u1","status":"SUCCEEDED"},{"id":"autogen_task1_u2","status":"SUCCEEDED"},{"id":"autogen_task1_alpha3","status":"SUCCEEDED"},{"id":"autogen_task1_u3","status":"SUCCEEDED"},{"id":"autogen_task1_bladder_cancer_tme","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_growth","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_killing","status":"SUCCEEDED"},{"id":"autogen_task1_effector_activation_by_cancer","status":"SUCCEEDED"},{"id":"autogen_task1_effector_activation_by_BCG","status":"SUCCEEDED"},{"id":"autogen_task1_effector_depletion_by_cancer","status":"SUCCEEDED"},{"id":"autogen_task1_effector_death","status":"SUCCEEDED"},{"id":"autogen_task1_BCG_death","status":"SUCCEEDED"},{"id":"autogen_task1_BCG_killing_by_effector","status":"SUCCEEDED"},{"id":"autogen_task1_checkpoint_source","status":"SUCCEEDED"},{"id":"autogen_task1_checkpoint_decay","status":"SUCCEEDED"}]}]},{"location":"Saad2017.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 2 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 2\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 3: Saad2017.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":0.585034,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.111498,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.181395,"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":0.086845,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_a1","status":"SUCCEEDED"},{"id":"autogen_task1_a2","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_alpha2","status":"SUCCEEDED"},{"id":"autogen_task1_u1","status":"SUCCEEDED"},{"id":"autogen_task1_u2","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_alpha3","status":"SUCCEEDED"},{"id":"autogen_task1_u3","status":"SUCCEEDED"},{"id":"autogen_task1_bladder_cancer_tme","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_growth","status":"SUCCEEDED"},{"id":"autogen_task1_cancer_killing","status":"SUCCEEDED"},{"id":"autogen_task1_effector_activation_by_cancer","status":"SUCCEEDED"},{"id":"autogen_task1_effector_activation_by_BCG","status":"SUCCEEDED"},{"id":"autogen_task1_effector_depletion_by_cancer","status":"SUCCEEDED"},{"id":"autogen_task1_effector_death","status":"SUCCEEDED"},{"id":"autogen_task1_BCG_source__therapy","status":"SUCCEEDED"},{"id":"autogen_task1_BCG_death","status":"SUCCEEDED"},{"id":"autogen_task1_BCG_killing_by_effector","status":"SUCCEEDED"},{"id":"autogen_task1_checkpoint_source","status":"SUCCEEDED"},{"id":"autogen_task1_checkpoint_decay","status":"SUCCEEDED"}]}]}]}