{"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    476      0 --:--:-- --:--:-- --:--:--   477\n\r100  614k  100  614k    0     0  1375k      0 --:--:-- --:--:-- --:--:-- 1375k\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 (24.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/rawLog.txt\nCompleted 6.2 KiB/6.2 KiB (83.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000526_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000526_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/reports.h5 (deflated 7%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/376.8 KiB (5.3 MiB/s) with 1 file(s) remaining\rCompleted 376.8 KiB/376.8 KiB (3.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/outputs/reports.h5\nCompleted 256.0 KiB/394.3 KiB (5.4 MiB/s) with 4 file(s) remaining\rCompleted 266.5 KiB/394.3 KiB (2.6 MiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/outputs/plots.zip\nCompleted 266.5 KiB/394.3 KiB (2.6 MiB/s) with 3 file(s) remaining\rCompleted 282.2 KiB/394.3 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000526_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/outputs/BIOMD0000000526_url.sedml/autogen_plot_for_task1.pdf\nCompleted 282.2 KiB/394.3 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 391.6 KiB/394.3 KiB (3.1 MiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/output.zip\nCompleted 391.6 KiB/394.3 KiB (3.1 MiB/s) with 1 file(s) remaining\rCompleted 394.3 KiB/394.3 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000526-biopax2.owl  \n  inflating: contents/BIOMD0000000526-biopax3.owl  \n  inflating: contents/BIOMD0000000526-matlab.m  \n  inflating: contents/BIOMD0000000526.m  \n  inflating: contents/BIOMD0000000526.ode  \n  inflating: contents/BIOMD0000000526.pdf  \n  inflating: contents/BIOMD0000000526.png  \n  inflating: contents/BIOMD0000000526.sci  \n  inflating: contents/BIOMD0000000526.svg  \n  inflating: contents/BIOMD0000000526.vcml  \n  inflating: contents/BIOMD0000000526_url.sedml  \n  inflating: contents/BIOMD0000000526_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 56.5 KiB/1.0 MiB (631.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000526-biopax3.owl to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526-biopax3.owl\nCompleted 56.5 KiB/1.0 MiB (631.0 KiB/s) with 15 file(s) remaining\rCompleted 65.6 KiB/1.0 MiB (601.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000526-matlab.m to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526-matlab.m\nCompleted 65.6 KiB/1.0 MiB (601.2 KiB/s) with 14 file(s) remaining\rCompleted 74.7 KiB/1.0 MiB (625.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000526.m to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526.m\nCompleted 74.7 KiB/1.0 MiB (625.9 KiB/s) with 13 file(s) remaining\rCompleted 110.6 KiB/1.0 MiB (814.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000526-biopax2.owl to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526-biopax2.owl\nCompleted 110.6 KiB/1.0 MiB (814.9 KiB/s) with 12 file(s) remaining\rCompleted 112.5 KiB/1.0 MiB (748.7 KiB/s) with 12 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/manifest.xml\nCompleted 112.5 KiB/1.0 MiB (748.7 KiB/s) with 11 file(s) remaining\rCompleted 368.5 KiB/1.0 MiB (2.4 MiB/s) with 11 file(s) remaining  \rCompleted 433.8 KiB/1.0 MiB (2.7 MiB/s) with 11 file(s) remaining  \rupload: contents/BIOMD0000000526.svg to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526.svg\nCompleted 433.8 KiB/1.0 MiB (2.7 MiB/s) with 10 file(s) remaining\rCompleted 465.2 KiB/1.0 MiB (2.8 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000526_url.sedml to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526_url.sedml\nCompleted 465.2 KiB/1.0 MiB (2.8 MiB/s) with 9 file(s) remaining\rCompleted 471.7 KiB/1.0 MiB (2.8 MiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/metadata.rdf\nCompleted 471.7 KiB/1.0 MiB (2.8 MiB/s) with 8 file(s) remaining\rCompleted 517.0 KiB/1.0 MiB (2.9 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000526_url.xml to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526_url.xml\nCompleted 517.0 KiB/1.0 MiB (2.9 MiB/s) with 7 file(s) remaining\rCompleted 576.6 KiB/1.0 MiB (2.9 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000526.vcml to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526.vcml\nCompleted 576.6 KiB/1.0 MiB (2.9 MiB/s) with 6 file(s) remaining\rCompleted 583.0 KiB/1.0 MiB (2.9 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000526.sci to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526.sci\nCompleted 583.0 KiB/1.0 MiB (2.9 MiB/s) with 5 file(s) remaining\rCompleted 589.3 KiB/1.0 MiB (2.8 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000526.ode to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526.ode\nCompleted 589.3 KiB/1.0 MiB (2.8 MiB/s) with 4 file(s) remaining\rCompleted 589.8 KiB/1.0 MiB (2.8 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/curation_notes.txt\nCompleted 589.8 KiB/1.0 MiB (2.8 MiB/s) with 3 file(s) remaining\rCompleted 784.0 KiB/1.0 MiB (3.6 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000526.png to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526.png\nCompleted 784.0 KiB/1.0 MiB (3.6 MiB/s) with 2 file(s) remaining\rCompleted 805.9 KiB/1.0 MiB (3.5 MiB/s) with 2 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/curation_image.png\nCompleted 805.9 KiB/1.0 MiB (3.5 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/1.0 MiB (4.2 MiB/s) with 1 file(s) remaining  \rupload: contents/BIOMD0000000526.pdf to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/contents/BIOMD0000000526.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (138.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471111449c0d898ffdee1e1/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000526_url.sedml\ncreating dataset /BIOMD0000000526_url.sedml/autogen_plot_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-a2bbffdb-1786b8d4-3df6-fc693e-eb45fe, chunk_size: (19, 1001)\ncreating dataset /BIOMD0000000526_url.sedml/autogen_report_for_task1, shape: (54, 1001), type: float64\ndataset created, uuid: d-a2bbffdb-1786b8d4-34f4-0188a9-796ca2, chunk_size: (54, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000526_url.sedml\ncreating attribute uri in /BIOMD0000000526_url.sedml\ncreating attribute _type in /BIOMD0000000526_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000526_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000526_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000526_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000526_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000526_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000526_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000526_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000526_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000526_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000526_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000526_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000526_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000526_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000526_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000526_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000526_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000526_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000526_url.sedml\ncreate_links: /BIOMD0000000526_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000526_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000526_url.sedml/autogen_plot_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000526_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000526_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000526_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000526_url.sedml/autogen_report_for_task1, shape: (54, 1001), type: float64\niterating over chunks for /BIOMD0000000526_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 54, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000526_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471111449c0d898ffdee1e1\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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.\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":2.246417,"sedDocuments":[{"location":"BIOMD0000000526_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  BIOMD0000000526_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 54 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 18 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000526_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":1.599158,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.281574,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.41367,"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_kD216trans_p55","status":"SUCCEEDED"},{"id":"autogen_task1_kD216trans_p43","status":"SUCCEEDED"},{"id":"autogen_task1_kD374","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_task1_reaction_14","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_15","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_16","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_17","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_18","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_19","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.732343,"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"}]}]}]}