{"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    451      0 --:--:-- --:--:-- --:--:--   449\n\r100  418k  100  418k    0     0   894k      0 --:--:-- --:--:-- --:--:--  894k\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 (26.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/rawLog.txt\nCompleted 5.2 KiB/5.2 KiB (68.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/BIOMD0000000523_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000523_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 8%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/340.9 KiB (5.4 MiB/s) with 1 file(s) remaining\rCompleted 340.9 KiB/340.9 KiB (3.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/outputs/reports.h5\nCompleted 256.0 KiB/356.8 KiB (6.0 MiB/s) with 4 file(s) remaining\rCompleted 327.7 KiB/356.8 KiB (3.3 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/output.zip\nCompleted 327.7 KiB/356.8 KiB (3.3 MiB/s) with 3 file(s) remaining\rCompleted 330.4 KiB/356.8 KiB (3.0 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/rawLog.txt\nCompleted 330.4 KiB/356.8 KiB (3.0 MiB/s) with 2 file(s) remaining\rCompleted 346.2 KiB/356.8 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000523_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/outputs/BIOMD0000000523_url.sedml/autogen_plot_for_task1.pdf\nCompleted 346.2 KiB/356.8 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 356.8 KiB/356.8 KiB (2.8 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000523-biopax2.owl  \n  inflating: contents/BIOMD0000000523-biopax3.owl  \n  inflating: contents/BIOMD0000000523-matlab.m  \n  inflating: contents/BIOMD0000000523.m  \n  inflating: contents/BIOMD0000000523.ode  \n  inflating: contents/BIOMD0000000523.pdf  \n  inflating: contents/BIOMD0000000523.png  \n  inflating: contents/BIOMD0000000523.sci  \n  inflating: contents/BIOMD0000000523.svg  \n  inflating: contents/BIOMD0000000523.vcml  \n  inflating: contents/BIOMD0000000523_url.sedml  \n  inflating: contents/BIOMD0000000523_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 27.8 KiB/716.8 KiB (375.9 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000523-biopax2.owl to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523-biopax2.owl\nCompleted 27.8 KiB/716.8 KiB (375.9 KiB/s) with 15 file(s) remaining\rCompleted 35.5 KiB/716.8 KiB (321.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000523-matlab.m to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523-matlab.m\nCompleted 35.5 KiB/716.8 KiB (321.0 KiB/s) with 14 file(s) remaining\rCompleted 40.9 KiB/716.8 KiB (350.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000523.sci to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523.sci\nCompleted 40.9 KiB/716.8 KiB (350.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000523.svg to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523.svg\nCompleted 40.9 KiB/716.8 KiB (350.1 KiB/s) with 12 file(s) remaining\rCompleted 48.6 KiB/716.8 KiB (368.2 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000523.m to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523.m\nCompleted 48.6 KiB/716.8 KiB (368.2 KiB/s) with 11 file(s) remaining\rCompleted 101.2 KiB/716.8 KiB (705.2 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000523.vcml to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523.vcml\nCompleted 101.2 KiB/716.8 KiB (705.2 KiB/s) with 10 file(s) remaining\rCompleted 127.8 KiB/716.8 KiB (847.9 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000523_url.sedml to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523_url.sedml\nCompleted 127.8 KiB/716.8 KiB (847.9 KiB/s) with 9 file(s) remaining\rCompleted 165.9 KiB/716.8 KiB (1.1 MiB/s) with 9 file(s) remaining  \rupload: contents/BIOMD0000000523_url.xml to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523_url.xml\nCompleted 165.9 KiB/716.8 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 166.5 KiB/716.8 KiB (1.0 MiB/s) with 8 file(s) remaining\rCompleted 189.2 KiB/716.8 KiB (1.1 MiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/curation_image.png\nCompleted 189.2 KiB/716.8 KiB (1.1 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/curation_notes.txt\nCompleted 189.2 KiB/716.8 KiB (1.1 MiB/s) with 6 file(s) remaining\rCompleted 191.0 KiB/716.8 KiB (1.1 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/manifest.xml\nCompleted 191.0 KiB/716.8 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 197.5 KiB/716.8 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/metadata.rdf\nCompleted 197.5 KiB/716.8 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 202.7 KiB/716.8 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000523.ode to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523.ode\nCompleted 202.7 KiB/716.8 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 245.1 KiB/716.8 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000523-biopax3.owl to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523-biopax3.owl\nCompleted 245.1 KiB/716.8 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 496.7 KiB/716.8 KiB (2.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000523.png to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523.png\nCompleted 496.7 KiB/716.8 KiB (2.4 MiB/s) with 1 file(s) remaining\rCompleted 716.8 KiB/716.8 KiB (3.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000523.pdf to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/contents/BIOMD0000000523.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (140.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471110b0dcacb55678c8294/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000523_url.sedml\ncreating dataset /BIOMD0000000523_url.sedml/autogen_plot_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-1f7a42d4-33923e5d-dca3-1626e7-06876e, chunk_size: (19, 1001)\ncreating dataset /BIOMD0000000523_url.sedml/autogen_report_for_task1, shape: (45, 1001), type: float64\ndataset created, uuid: d-1f7a42d4-33923e5d-3044-781fff-82dbab, chunk_size: (45, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000523_url.sedml\ncreating attribute uri in /BIOMD0000000523_url.sedml\ncreating attribute _type in /BIOMD0000000523_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000523_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000523_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000523_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000523_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000523_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000523_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000523_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000523_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000523_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000523_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000523_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000523_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000523_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000523_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000523_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000523_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000523_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000523_url.sedml\ncreate_links: /BIOMD0000000523_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000523_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000523_url.sedml/autogen_plot_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000523_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000523_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000523_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000523_url.sedml/autogen_report_for_task1, shape: (45, 1001), type: float64\niterating over chunks for /BIOMD0000000523_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 45, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000523_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471110b0dcacb55678c8294\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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":19.72034,"sedDocuments":[{"location":"BIOMD0000000523_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  BIOMD0000000523_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 45 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 18 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000523_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":19.386329,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":18.413592,"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":0.317473,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_CD95","status":"SUCCEEDED"},{"id":"autogen_task1_FADD","status":"SUCCEEDED"},{"id":"autogen_task1_p55free","status":"SUCCEEDED"},{"id":"autogen_task1_Bid","status":"SUCCEEDED"},{"id":"autogen_task1_PrNES_mCherry","status":"SUCCEEDED"},{"id":"autogen_task1_PrER_mGFP","status":"SUCCEEDED"},{"id":"autogen_task1_DISC","status":"SUCCEEDED"},{"id":"autogen_task1_DISCp55","status":"SUCCEEDED"},{"id":"autogen_task1_p30","status":"SUCCEEDED"},{"id":"autogen_task1_p43","status":"SUCCEEDED"},{"id":"autogen_task1_p18","status":"SUCCEEDED"},{"id":"autogen_task1_p18inactive","status":"SUCCEEDED"},{"id":"autogen_task1_tBid","status":"SUCCEEDED"},{"id":"autogen_task1_PrNES","status":"SUCCEEDED"},{"id":"autogen_task1_mCherry","status":"SUCCEEDED"},{"id":"autogen_task1_PrER","status":"SUCCEEDED"},{"id":"autogen_task1_mGFP","status":"SUCCEEDED"},{"id":"autogen_task1_CD95L","status":"SUCCEEDED"},{"id":"autogen_task1_kon_FADD","status":"SUCCEEDED"},{"id":"autogen_task1_koff_FADD","status":"SUCCEEDED"},{"id":"autogen_task1_kDISC","status":"SUCCEEDED"},{"id":"autogen_task1_kD216","status":"SUCCEEDED"},{"id":"autogen_task1_kD374trans_p55","status":"SUCCEEDED"},{"id":"autogen_task1_kD374trans_p43","status":"SUCCEEDED"},{"id":"autogen_task1_kdiss_p18","status":"SUCCEEDED"},{"id":"autogen_task1_kBid","status":"SUCCEEDED"},{"id":"autogen_task1_kD374probe","status":"SUCCEEDED"},{"id":"autogen_task1_KDR","status":"SUCCEEDED"},{"id":"autogen_task1_KDL","status":"SUCCEEDED"},{"id":"autogen_task1_CD95act","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_task1_reaction_9","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_10","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_11","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_12","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_13","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.502002,"curves":[{"id":"autogen_curve_task1_CD95","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FADD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_p55free","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Bid","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PrNES_mCherry","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PrER_mGFP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DISC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DISCp55","status":"SUCCEEDED"},{"id":"autogen_curve_task1_p30","status":"SUCCEEDED"},{"id":"autogen_curve_task1_p43","status":"SUCCEEDED"},{"id":"autogen_curve_task1_p18","status":"SUCCEEDED"},{"id":"autogen_curve_task1_p18inactive","status":"SUCCEEDED"},{"id":"autogen_curve_task1_tBid","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PrNES","status":"SUCCEEDED"},{"id":"autogen_curve_task1_mCherry","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PrER","status":"SUCCEEDED"},{"id":"autogen_curve_task1_mGFP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CD95L","status":"SUCCEEDED"}]}]}]}