{"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    432      0 --:--:-- --:--:-- --:--:--   433\n\r100  242k  100  242k    0     0   450k      0 --:--:-- --:--:-- --:--:--  450k\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 (21.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (31.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 78%)\n  adding: outputs/BIOMD0000000360_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000360_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 200.2 KiB/200.2 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/outputs/reports.h5\nCompleted 188.7 KiB/209.1 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/output.zip\nCompleted 188.7 KiB/209.1 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 195.9 KiB/209.1 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/outputs/plots.zip\nCompleted 195.9 KiB/209.1 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 206.5 KiB/209.1 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000360_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/outputs/BIOMD0000000360_url.sedml/autogen_plot_for_task1.pdf\nCompleted 206.5 KiB/209.1 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 209.1 KiB/209.1 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000360-biopax2.owl  \n  inflating: contents/BIOMD0000000360-biopax3.owl  \n  inflating: contents/BIOMD0000000360-matlab.m  \n  inflating: contents/BIOMD0000000360-octave.m  \n  inflating: contents/BIOMD0000000360.m  \n  inflating: contents/BIOMD0000000360.ode  \n  inflating: contents/BIOMD0000000360.pdf  \n  inflating: contents/BIOMD0000000360.png  \n  inflating: contents/BIOMD0000000360.sci  \n  inflating: contents/BIOMD0000000360.svg  \n  inflating: contents/BIOMD0000000360.vcml  \n  inflating: contents/BIOMD0000000360_url.sedml  \n  inflating: contents/BIOMD0000000360_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 16.3 KiB/433.3 KiB (217.8 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000360-biopax2.owl to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360-biopax2.owl\nCompleted 16.3 KiB/433.3 KiB (217.8 KiB/s) with 16 file(s) remaining\rCompleted 22.4 KiB/433.3 KiB (196.6 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000360-matlab.m to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360-matlab.m\nCompleted 22.4 KiB/433.3 KiB (196.6 KiB/s) with 15 file(s) remaining\rCompleted 28.6 KiB/433.3 KiB (244.8 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000360-octave.m to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360-octave.m\nCompleted 28.6 KiB/433.3 KiB (244.8 KiB/s) with 14 file(s) remaining\rCompleted 33.2 KiB/433.3 KiB (277.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000360.sci to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360.sci\nCompleted 33.2 KiB/433.3 KiB (277.4 KiB/s) with 13 file(s) remaining\rCompleted 80.6 KiB/433.3 KiB (615.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000360.png to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360.png\nCompleted 80.6 KiB/433.3 KiB (615.8 KiB/s) with 12 file(s) remaining\rCompleted 80.7 KiB/433.3 KiB (574.5 KiB/s) with 12 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/curation_notes.txt\nCompleted 80.7 KiB/433.3 KiB (574.5 KiB/s) with 11 file(s) remaining\rCompleted 104.0 KiB/433.3 KiB (701.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000360.svg to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360.svg\nCompleted 104.0 KiB/433.3 KiB (701.8 KiB/s) with 10 file(s) remaining\rCompleted 132.4 KiB/433.3 KiB (863.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000360.vcml to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360.vcml\nCompleted 132.4 KiB/433.3 KiB (863.6 KiB/s) with 9 file(s) remaining\rCompleted 134.4 KiB/433.3 KiB (827.4 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/manifest.xml\nCompleted 134.4 KiB/433.3 KiB (827.4 KiB/s) with 8 file(s) remaining\rCompleted 146.8 KiB/433.3 KiB (880.0 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000360_url.sedml to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360_url.sedml\nCompleted 146.8 KiB/433.3 KiB (880.0 KiB/s) with 7 file(s) remaining\rCompleted 148.0 KiB/433.3 KiB (857.9 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/metadata.rdf\nCompleted 148.0 KiB/433.3 KiB (857.9 KiB/s) with 6 file(s) remaining\rCompleted 167.3 KiB/433.3 KiB (929.9 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000360_url.xml to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360_url.xml\nCompleted 167.3 KiB/433.3 KiB (929.9 KiB/s) with 5 file(s) remaining\rCompleted 193.5 KiB/433.3 KiB (1.0 MiB/s) with 5 file(s) remaining  \rupload: contents/BIOMD0000000360-biopax3.owl to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360-biopax3.owl\nCompleted 193.5 KiB/433.3 KiB (1.0 MiB/s) with 4 file(s) remaining\rCompleted 371.8 KiB/433.3 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000360.pdf to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360.pdf\nCompleted 371.8 KiB/433.3 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 378.0 KiB/433.3 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000360.m to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360.m\nCompleted 378.0 KiB/433.3 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 381.9 KiB/433.3 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000360.ode to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/BIOMD0000000360.ode\nCompleted 381.9 KiB/433.3 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 433.3 KiB/433.3 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (116.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ba60dcacb55678bb75d/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000360_url.sedml\ncreating dataset /BIOMD0000000360_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-12d23a76-73fb050e-3821-bb50b7-382356, chunk_size: (10, 1001)\ncreating dataset /BIOMD0000000360_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-12d23a76-73fb050e-8c30-26bc7d-bd4b99, chunk_size: (19, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000360_url.sedml\ncreating attribute uri in /BIOMD0000000360_url.sedml\ncreating attribute _type in /BIOMD0000000360_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000360_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000360_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000360_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000360_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000360_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000360_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000360_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000360_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000360_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000360_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000360_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000360_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000360_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000360_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000360_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000360_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000360_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000360_url.sedml\ncreate_links: /BIOMD0000000360_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000360_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000360_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000360_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000360_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000360_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000360_url.sedml/autogen_report_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000360_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000360_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710ba60dcacb55678bb75d\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":18.268003,"sedDocuments":[{"location":"BIOMD0000000360_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  BIOMD0000000360_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 19 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 9 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000360_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":17.993335,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":17.27311,"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":0.210195,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_VIIa_TF","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_VIIa_TF_X","status":"SUCCEEDED"},{"id":"autogen_task1_VIIa_TF_Xa","status":"SUCCEEDED"},{"id":"autogen_task1_Xa","status":"SUCCEEDED"},{"id":"autogen_task1_TFPI","status":"SUCCEEDED"},{"id":"autogen_task1_Xa_TFPI","status":"SUCCEEDED"},{"id":"autogen_task1_Xa_TFPI_VIIa_TF","status":"SUCCEEDED"},{"id":"autogen_task1_VIIa_TF_Xa_TFPI","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.388771,"curves":[{"id":"autogen_curve_task1_VIIa_TF","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_VIIa_TF_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_VIIa_TF_Xa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Xa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_TFPI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Xa_TFPI","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Xa_TFPI_VIIa_TF","status":"SUCCEEDED"},{"id":"autogen_curve_task1_VIIa_TF_Xa_TFPI","status":"SUCCEEDED"}]}]}]}