{"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    427      0 --:--:-- --:--:-- --:--:--   429\n\r100  455k  100  455k    0     0   997k      0 --:--:-- --:--:-- --:--:--  997k\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 (24.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/rawLog.txt\nCompleted 6.5 KiB/6.5 KiB (74.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 86%)\n  adding: outputs/BIOMD0000000211_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000211_url.sedml/autogen_plot_for_task1.pdf (deflated 21%)\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/434.8 KiB (6.3 MiB/s) with 1 file(s) remaining\rCompleted 434.8 KiB/434.8 KiB (3.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/outputs/reports.h5\nCompleted 256.0 KiB/446.6 KiB (5.2 MiB/s) with 4 file(s) remaining\rCompleted 417.8 KiB/446.6 KiB (3.5 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/output.zip\nCompleted 417.8 KiB/446.6 KiB (3.5 MiB/s) with 3 file(s) remaining\rCompleted 420.5 KiB/446.6 KiB (3.3 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/rawLog.txt\nCompleted 420.5 KiB/446.6 KiB (3.3 MiB/s) with 2 file(s) remaining\rCompleted 431.9 KiB/446.6 KiB (3.3 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/outputs/plots.zip\nCompleted 431.9 KiB/446.6 KiB (3.3 MiB/s) with 1 file(s) remaining\rCompleted 446.6 KiB/446.6 KiB (3.4 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000211_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/outputs/BIOMD0000000211_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/BIOMD0000000211-biopax2.owl  \n  inflating: contents/BIOMD0000000211-biopax3.owl  \n  inflating: contents/BIOMD0000000211-matlab.m  \n  inflating: contents/BIOMD0000000211-octave.m  \n  inflating: contents/BIOMD0000000211.m  \n  inflating: contents/BIOMD0000000211.ode  \n  inflating: contents/BIOMD0000000211.pdf  \n  inflating: contents/BIOMD0000000211.png  \n  inflating: contents/BIOMD0000000211.svg  \n  inflating: contents/BIOMD0000000211_url.sedml  \n  inflating: contents/BIOMD0000000211_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 77.6 KiB/983.8 KiB (918.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000211-biopax2.owl to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211-biopax2.owl\nCompleted 77.6 KiB/983.8 KiB (918.1 KiB/s) with 14 file(s) remaining\rCompleted 333.6 KiB/983.8 KiB (2.8 MiB/s) with 14 file(s) remaining \rCompleted 367.9 KiB/983.8 KiB (2.5 MiB/s) with 14 file(s) remaining \rupload: contents/BIOMD0000000211_url.sedml to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211_url.sedml\nCompleted 367.9 KiB/983.8 KiB (2.5 MiB/s) with 13 file(s) remaining\rCompleted 384.8 KiB/983.8 KiB (2.4 MiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000211.ode to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211.ode\nCompleted 384.8 KiB/983.8 KiB (2.4 MiB/s) with 12 file(s) remaining\rCompleted 405.0 KiB/983.8 KiB (2.5 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000211-octave.m to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211-octave.m\nCompleted 405.0 KiB/983.8 KiB (2.5 MiB/s) with 11 file(s) remaining\rCompleted 508.5 KiB/983.8 KiB (3.1 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000211-biopax3.owl to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211-biopax3.owl\nCompleted 508.5 KiB/983.8 KiB (3.1 MiB/s) with 10 file(s) remaining\rCompleted 608.7 KiB/983.8 KiB (3.6 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000211_url.xml to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211_url.xml\nCompleted 608.7 KiB/983.8 KiB (3.6 MiB/s) with 9 file(s) remaining\rCompleted 654.5 KiB/983.8 KiB (3.8 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000211.pdf to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211.pdf\nCompleted 654.5 KiB/983.8 KiB (3.8 MiB/s) with 8 file(s) remaining\rCompleted 853.8 KiB/983.8 KiB (4.9 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000211.png to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211.png\nCompleted 853.8 KiB/983.8 KiB (4.9 MiB/s) with 7 file(s) remaining\rCompleted 874.0 KiB/983.8 KiB (4.7 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000211.m to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211.m\nCompleted 874.0 KiB/983.8 KiB (4.7 MiB/s) with 6 file(s) remaining\rCompleted 921.4 KiB/983.8 KiB (4.5 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000211.svg to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211.svg\nCompleted 921.4 KiB/983.8 KiB (4.5 MiB/s) with 5 file(s) remaining\rCompleted 956.5 KiB/983.8 KiB (4.6 MiB/s) with 5 file(s) remaining\rCompleted 976.7 KiB/983.8 KiB (4.7 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000211-matlab.m to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/BIOMD0000000211-matlab.m\nCompleted 976.7 KiB/983.8 KiB (4.7 MiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/curation_image.png\nCompleted 976.7 KiB/983.8 KiB (4.7 MiB/s) with 3 file(s) remaining\rCompleted 978.4 KiB/983.8 KiB (4.3 MiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/manifest.xml\nCompleted 978.4 KiB/983.8 KiB (4.3 MiB/s) with 2 file(s) remaining\rCompleted 983.7 KiB/983.8 KiB (4.2 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/metadata.rdf\nCompleted 983.7 KiB/983.8 KiB (4.2 MiB/s) with 1 file(s) remaining\rCompleted 983.8 KiB/983.8 KiB (3.9 MiB/s) with 1 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/contents/curation_notes.txt\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.7 KiB/8.7 KiB (92.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c467195afd5df1769113/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000211_url.sedml\ncreating dataset /BIOMD0000000211_url.sedml/autogen_plot_for_task1, shape: (28, 1001), type: float64\ndataset created, uuid: d-e32ad6ec-32a444fc-1b3e-010e74-790f51, chunk_size: (28, 1001)\ncreating dataset /BIOMD0000000211_url.sedml/autogen_report_for_task1, shape: (57, 1001), type: float64\ndataset created, uuid: d-e32ad6ec-32a444fc-ce7b-075aaf-e82310, chunk_size: (57, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000211_url.sedml\ncreating attribute uri in /BIOMD0000000211_url.sedml\ncreating attribute _type in /BIOMD0000000211_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000211_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000211_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000211_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000211_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000211_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000211_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000211_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000211_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000211_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000211_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000211_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000211_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000211_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000211_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000211_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000211_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000211_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000211_url.sedml\ncreate_links: /BIOMD0000000211_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000211_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000211_url.sedml/autogen_plot_for_task1, shape: (28, 1001), type: float64\niterating over chunks for /BIOMD0000000211_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 28, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000211_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000211_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000211_url.sedml/autogen_report_for_task1, shape: (57, 1001), type: float64\niterating over chunks for /BIOMD0000000211_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 57, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000211_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c467195afd5df1769113\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 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.\nProcess 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":25.699588,"sedDocuments":[{"location":"BIOMD0000000211_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  BIOMD0000000211_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 57 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 27 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000211_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":25.29765,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":23.92077,"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":0.490933,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_task1_species_2","status":"SUCCEEDED"},{"id":"autogen_task1_species_3","status":"SUCCEEDED"},{"id":"autogen_task1_species_4","status":"SUCCEEDED"},{"id":"autogen_task1_species_5","status":"SUCCEEDED"},{"id":"autogen_task1_species_6","status":"SUCCEEDED"},{"id":"autogen_task1_species_7","status":"SUCCEEDED"},{"id":"autogen_task1_species_8","status":"SUCCEEDED"},{"id":"autogen_task1_species_9","status":"SUCCEEDED"},{"id":"autogen_task1_species_10","status":"SUCCEEDED"},{"id":"autogen_task1_species_11","status":"SUCCEEDED"},{"id":"autogen_task1_species_12","status":"SUCCEEDED"},{"id":"autogen_task1_species_13","status":"SUCCEEDED"},{"id":"autogen_task1_species_14","status":"SUCCEEDED"},{"id":"autogen_task1_species_15","status":"SUCCEEDED"},{"id":"autogen_task1_species_16","status":"SUCCEEDED"},{"id":"autogen_task1_species_17","status":"SUCCEEDED"},{"id":"autogen_task1_species_18","status":"SUCCEEDED"},{"id":"autogen_task1_species_19","status":"SUCCEEDED"},{"id":"autogen_task1_species_20","status":"SUCCEEDED"},{"id":"autogen_task1_species_21","status":"SUCCEEDED"},{"id":"autogen_task1_species_22","status":"SUCCEEDED"},{"id":"autogen_task1_species_23","status":"SUCCEEDED"},{"id":"autogen_task1_species_24","status":"SUCCEEDED"},{"id":"autogen_task1_species_25","status":"SUCCEEDED"},{"id":"autogen_task1_species_26","status":"SUCCEEDED"},{"id":"autogen_task1_species_27","status":"SUCCEEDED"},{"id":"autogen_task1_RaHXK","status":"SUCCEEDED"},{"id":"autogen_task1_RaPFK","status":"SUCCEEDED"},{"id":"autogen_task1_RaPYK","status":"SUCCEEDED"},{"id":"autogen_task1_RaPGAM","status":"SUCCEEDED"},{"id":"autogen_task1_RaENO","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_1","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_2","status":"SUCCEEDED"},{"id":"autogen_task1_compartment_3","status":"SUCCEEDED"},{"id":"autogen_task1_vGT","status":"SUCCEEDED"},{"id":"autogen_task1_vHK","status":"SUCCEEDED"},{"id":"autogen_task1_vPGI","status":"SUCCEEDED"},{"id":"autogen_task1_vPFK","status":"SUCCEEDED"},{"id":"autogen_task1_vALD","status":"SUCCEEDED"},{"id":"autogen_task1_vTPI","status":"SUCCEEDED"},{"id":"autogen_task1_vGAPDH","status":"SUCCEEDED"},{"id":"autogen_task1_vGPDH","status":"SUCCEEDED"},{"id":"autogen_task1_vGPO","status":"SUCCEEDED"},{"id":"autogen_task1_vPT","status":"SUCCEEDED"},{"id":"autogen_task1_vPGK","status":"SUCCEEDED"},{"id":"autogen_task1_vPK","status":"SUCCEEDED"},{"id":"autogen_task1_vAU","status":"SUCCEEDED"},{"id":"autogen_task1_vGK","status":"SUCCEEDED"},{"id":"autogen_task1_vPGM","status":"SUCCEEDED"},{"id":"autogen_task1_vENO","status":"SUCCEEDED"},{"id":"autogen_task1_vAKc","status":"SUCCEEDED"},{"id":"autogen_task1_vAKg","status":"SUCCEEDED"},{"id":"autogen_task1_vPGT","status":"SUCCEEDED"},{"id":"autogen_task1_vANTI","status":"SUCCEEDED"},{"id":"autogen_task1_vGlyT","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.702612,"curves":[{"id":"autogen_curve_task1_species_1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_5","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_6","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_7","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_8","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_9","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_10","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_11","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_12","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_13","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_14","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_15","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_16","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_17","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_18","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_19","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_20","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_21","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_22","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_23","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_24","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_25","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_26","status":"SUCCEEDED"},{"id":"autogen_curve_task1_species_27","status":"SUCCEEDED"}]}]}]}