{"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    461      0 --:--:-- --:--:-- --:--:--   460\n\r100  428k  100  428k    0     0   970k      0 --:--:-- --:--:-- --:--:--  970k\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 (20.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/rawLog.txt\nCompleted 6.4 KiB/6.4 KiB (69.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 85%)\n  adding: outputs/BIOMD0000000336_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000336_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 7%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/449.7 KiB (5.8 MiB/s) with 1 file(s) remaining\rCompleted 449.7 KiB/449.7 KiB (3.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/outputs/reports.h5\nCompleted 256.0 KiB/449.7 KiB (5.8 MiB/s) with 4 file(s) remaining\rCompleted 428.9 KiB/449.7 KiB (3.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/output.zip\nCompleted 428.9 KiB/449.7 KiB (3.0 MiB/s) with 3 file(s) remaining\rCompleted 436.2 KiB/449.7 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/outputs/plots.zip\nCompleted 436.2 KiB/449.7 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 439.0 KiB/449.7 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/rawLog.txt\nCompleted 439.0 KiB/449.7 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 449.7 KiB/449.7 KiB (2.6 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000336_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/outputs/BIOMD0000000336_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000336-biopax2.owl  \n  inflating: contents/BIOMD0000000336-biopax3.owl  \n  inflating: contents/BIOMD0000000336-matlab.m  \n  inflating: contents/BIOMD0000000336-octave.m  \n  inflating: contents/BIOMD0000000336.m  \n  inflating: contents/BIOMD0000000336.ode  \n  inflating: contents/BIOMD0000000336.pdf  \n  inflating: contents/BIOMD0000000336.png  \n  inflating: contents/BIOMD0000000336.svg  \n  inflating: contents/BIOMD0000000336_url.sedml  \n  inflating: contents/BIOMD0000000336_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 60.9 KiB/787.9 KiB (611.9 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000336-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336-biopax3.owl\nCompleted 60.9 KiB/787.9 KiB (611.9 KiB/s) with 14 file(s) remaining\rCompleted 94.6 KiB/787.9 KiB (569.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000336_url.sedml to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336_url.sedml\nCompleted 94.6 KiB/787.9 KiB (569.5 KiB/s) with 13 file(s) remaining\rCompleted 104.2 KiB/787.9 KiB (617.2 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000336-matlab.m to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336-matlab.m\nCompleted 104.2 KiB/787.9 KiB (617.2 KiB/s) with 12 file(s) remaining\rCompleted 139.8 KiB/787.9 KiB (763.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000336-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336-biopax2.owl\nCompleted 139.8 KiB/787.9 KiB (763.5 KiB/s) with 11 file(s) remaining\rCompleted 149.5 KiB/787.9 KiB (807.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000336-octave.m to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336-octave.m\nCompleted 149.5 KiB/787.9 KiB (807.8 KiB/s) with 10 file(s) remaining\rCompleted 202.5 KiB/787.9 KiB (1.1 MiB/s) with 10 file(s) remaining  \rCompleted 240.9 KiB/787.9 KiB (1.2 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000336_url.xml to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336_url.xml\nCompleted 240.9 KiB/787.9 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/curation_image.png\nCompleted 240.9 KiB/787.9 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 246.0 KiB/787.9 KiB (1.2 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/metadata.rdf\nCompleted 246.0 KiB/787.9 KiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 301.5 KiB/787.9 KiB (1.5 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000336.svg to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336.svg\nCompleted 301.5 KiB/787.9 KiB (1.5 MiB/s) with 6 file(s) remaining\rCompleted 302.0 KiB/787.9 KiB (1.4 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/curation_notes.txt\nCompleted 302.0 KiB/787.9 KiB (1.4 MiB/s) with 5 file(s) remaining\rCompleted 303.7 KiB/787.9 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/manifest.xml\nCompleted 303.7 KiB/787.9 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 312.7 KiB/787.9 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000336.m to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336.m\nCompleted 312.7 KiB/787.9 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 558.5 KiB/787.9 KiB (1.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000336.pdf to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336.pdf\nCompleted 558.5 KiB/787.9 KiB (1.8 MiB/s) with 2 file(s) remaining\rCompleted 565.0 KiB/787.9 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000336.ode to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336.ode\nCompleted 565.0 KiB/787.9 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 787.9 KiB/787.9 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000336.png to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/contents/BIOMD0000000336.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.7 KiB/8.7 KiB (68.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b0b195afd5df175eb33/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000336_url.sedml\ncreating dataset /BIOMD0000000336_url.sedml/autogen_plot_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-c3912a7b-73e06ceb-5d38-6264f5-d18b1d, chunk_size: (19, 1001)\ncreating dataset /BIOMD0000000336_url.sedml/autogen_report_for_task1, shape: (62, 1001), type: float64\ndataset created, uuid: d-c3912a7b-73e06ceb-2ec6-104d5a-7d88d0, chunk_size: (62, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000336_url.sedml\ncreating attribute uri in /BIOMD0000000336_url.sedml\ncreating attribute _type in /BIOMD0000000336_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000336_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000336_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000336_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000336_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000336_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000336_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000336_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000336_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000336_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000336_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000336_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000336_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000336_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000336_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000336_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000336_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000336_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000336_url.sedml\ncreate_links: /BIOMD0000000336_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000336_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000336_url.sedml/autogen_plot_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000336_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000336_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000336_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000336_url.sedml/autogen_report_for_task1, shape: (62, 1001), type: float64\niterating over chunks for /BIOMD0000000336_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 62, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000336_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b0b195afd5df175eb33\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 metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.814182,"sedDocuments":[{"location":"BIOMD0000000336_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  BIOMD0000000336_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 62 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 18 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000336_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":1.390593,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.233027,"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":0.386928,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_IX","status":"SUCCEEDED"},{"id":"autogen_task1_IX_TF_VIIa","status":"SUCCEEDED"},{"id":"autogen_task1_TF_VIIa","status":"SUCCEEDED"},{"id":"autogen_task1_IXa","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_X_TF_VIIa","status":"SUCCEEDED"},{"id":"autogen_task1_Xa","status":"SUCCEEDED"},{"id":"autogen_task1_VIIIa_IXa","status":"SUCCEEDED"},{"id":"autogen_task1_X_VIIIa_IXa","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_Va","status":"SUCCEEDED"},{"id":"autogen_task1_VIII","status":"SUCCEEDED"},{"id":"autogen_task1_VIIIa","status":"SUCCEEDED"},{"id":"autogen_task1_IIa","status":"SUCCEEDED"},{"id":"autogen_task1_II","status":"SUCCEEDED"},{"id":"autogen_task1_II_Va_Xa","status":"SUCCEEDED"},{"id":"autogen_task1_Va_Xa","status":"SUCCEEDED"},{"id":"autogen_task1_mIIa","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_k11","status":"SUCCEEDED"},{"id":"autogen_task1_k12","status":"SUCCEEDED"},{"id":"autogen_task1_k13","status":"SUCCEEDED"},{"id":"autogen_task1_k14","status":"SUCCEEDED"},{"id":"autogen_task1_k15","status":"SUCCEEDED"},{"id":"autogen_task1_k16","status":"SUCCEEDED"},{"id":"autogen_task1_k17","status":"SUCCEEDED"},{"id":"autogen_task1_k18","status":"SUCCEEDED"},{"id":"autogen_task1_k19","status":"SUCCEEDED"},{"id":"autogen_task1_k20","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_IIa_plus_1_2mIIa","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R1b","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R2b","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_R3b","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"},{"id":"autogen_task1_R5","status":"SUCCEEDED"},{"id":"autogen_task1_R6","status":"SUCCEEDED"},{"id":"autogen_task1_R7","status":"SUCCEEDED"},{"id":"autogen_task1_R8","status":"SUCCEEDED"},{"id":"autogen_task1_R9","status":"SUCCEEDED"},{"id":"autogen_task1_R9b","status":"SUCCEEDED"},{"id":"autogen_task1_R10","status":"SUCCEEDED"},{"id":"autogen_task1_R11","status":"SUCCEEDED"},{"id":"autogen_task1_R12","status":"SUCCEEDED"},{"id":"autogen_task1_R7_atn","status":"SUCCEEDED"},{"id":"autogen_task1_R8_atn","status":"SUCCEEDED"},{"id":"autogen_task1_R4_atn","status":"SUCCEEDED"},{"id":"autogen_task1_VIIIa_IXa_degradation","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.608646,"curves":[{"id":"autogen_curve_task1_IX","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IX_TF_VIIa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_TF_VIIa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IXa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X_TF_VIIa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Xa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_VIIIa_IXa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X_VIIIa_IXa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_V","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Va","status":"SUCCEEDED"},{"id":"autogen_curve_task1_VIII","status":"SUCCEEDED"},{"id":"autogen_curve_task1_VIIIa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IIa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_II","status":"SUCCEEDED"},{"id":"autogen_curve_task1_II_Va_Xa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Va_Xa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_mIIa","status":"SUCCEEDED"}]}]}]}