{"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    433      0 --:--:-- --:--:-- --:--:--   433\n\r100  317k  100  317k    0     0   720k      0 --:--:-- --:--:-- --:--:--  720k\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 (25.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/rawLog.txt\nCompleted 4.5 KiB/4.5 KiB (45.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/BIOMD0000000199_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000199_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 233.1 KiB/233.1 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/outputs/reports.h5\nCompleted 8.7 KiB/243.3 KiB (120.5 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/outputs/plots.zip\nCompleted 8.7 KiB/243.3 KiB (120.5 KiB/s) with 3 file(s) remaining\rCompleted 21.7 KiB/243.3 KiB (201.8 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000199_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/outputs/BIOMD0000000199_url.sedml/autogen_plot_for_task1.pdf\nCompleted 21.7 KiB/243.3 KiB (201.8 KiB/s) with 2 file(s) remaining\rCompleted 24.4 KiB/243.3 KiB (203.7 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/rawLog.txt\nCompleted 24.4 KiB/243.3 KiB (203.7 KiB/s) with 1 file(s) remaining\rCompleted 243.3 KiB/243.3 KiB (1.9 MiB/s) with 1 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/output.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000199-biopax2.owl  \n  inflating: contents/BIOMD0000000199-biopax3.owl  \n  inflating: contents/BIOMD0000000199-matlab.m  \n  inflating: contents/BIOMD0000000199-octave.m  \n  inflating: contents/BIOMD0000000199.m  \n  inflating: contents/BIOMD0000000199.ode  \n  inflating: contents/BIOMD0000000199.pdf  \n  inflating: contents/BIOMD0000000199.png  \n  inflating: contents/BIOMD0000000199.svg  \n  inflating: contents/BIOMD0000000199_url.sedml  \n  inflating: contents/BIOMD0000000199_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 38.9 KiB/535.0 KiB (506.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000199-biopax3.owl to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199-biopax3.owl\nCompleted 38.9 KiB/535.0 KiB (506.2 KiB/s) with 14 file(s) remaining\rCompleted 45.0 KiB/535.0 KiB (399.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000199-matlab.m to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199-matlab.m\nCompleted 45.0 KiB/535.0 KiB (399.5 KiB/s) with 13 file(s) remaining\rCompleted 70.6 KiB/535.0 KiB (572.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000199-biopax2.owl to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199-biopax2.owl\nCompleted 70.6 KiB/535.0 KiB (572.7 KiB/s) with 12 file(s) remaining\rCompleted 76.8 KiB/535.0 KiB (566.2 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000199-octave.m to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199-octave.m\nCompleted 76.8 KiB/535.0 KiB (566.2 KiB/s) with 11 file(s) remaining\rCompleted 98.1 KiB/535.0 KiB (679.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000199_url.sedml to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199_url.sedml\nCompleted 98.1 KiB/535.0 KiB (679.7 KiB/s) with 10 file(s) remaining\rCompleted 123.5 KiB/535.0 KiB (843.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000199.svg to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199.svg\nCompleted 123.5 KiB/535.0 KiB (843.6 KiB/s) with 9 file(s) remaining\rCompleted 126.7 KiB/535.0 KiB (833.7 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/metadata.rdf\nCompleted 126.7 KiB/535.0 KiB (833.7 KiB/s) with 8 file(s) remaining\rCompleted 153.9 KiB/535.0 KiB (882.7 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000199_url.xml to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199_url.xml\nCompleted 153.9 KiB/535.0 KiB (882.7 KiB/s) with 7 file(s) remaining\rCompleted 154.0 KiB/535.0 KiB (869.6 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/curation_notes.txt\nCompleted 154.0 KiB/535.0 KiB (869.6 KiB/s) with 6 file(s) remaining\rCompleted 247.2 KiB/535.0 KiB (1.3 MiB/s) with 6 file(s) remaining  \rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/curation_image.png\nCompleted 247.2 KiB/535.0 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 332.1 KiB/535.0 KiB (1.7 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000199.png to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199.png\nCompleted 332.1 KiB/535.0 KiB (1.7 MiB/s) with 4 file(s) remaining\rCompleted 333.9 KiB/535.0 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/manifest.xml\nCompleted 333.9 KiB/535.0 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 340.0 KiB/535.0 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000199.m to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199.m\nCompleted 340.0 KiB/535.0 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 530.8 KiB/535.0 KiB (2.6 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000199.pdf to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199.pdf\nCompleted 530.8 KiB/535.0 KiB (2.6 MiB/s) with 1 file(s) remaining\rCompleted 535.0 KiB/535.0 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000199.ode to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/contents/BIOMD0000000199.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (126.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471098249c0d898ffddd926/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000199_url.sedml\ncreating dataset /BIOMD0000000199_url.sedml/autogen_plot_for_task1, shape: (16, 1001), type: float64\ndataset created, uuid: d-06c15340-a45b01e6-0655-e1c1fe-3b49cf, chunk_size: (16, 1001)\ncreating dataset /BIOMD0000000199_url.sedml/autogen_report_for_task1, shape: (37, 1001), type: float64\ndataset created, uuid: d-06c15340-a45b01e6-7f9b-699349-db9ebf, chunk_size: (37, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000199_url.sedml\ncreating attribute uri in /BIOMD0000000199_url.sedml\ncreating attribute _type in /BIOMD0000000199_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000199_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000199_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000199_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000199_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000199_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000199_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000199_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000199_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000199_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000199_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000199_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000199_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000199_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000199_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000199_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000199_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000199_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000199_url.sedml\ncreate_links: /BIOMD0000000199_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000199_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000199_url.sedml/autogen_plot_for_task1, shape: (16, 1001), type: float64\niterating over chunks for /BIOMD0000000199_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 16, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000199_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000199_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000199_url.sedml/autogen_report_for_task1, shape: (37, 1001), type: float64\niterating over chunks for /BIOMD0000000199_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 37, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000199_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471098249c0d898ffddd926\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 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 metadata in the COMBINE archive ... succeeded.\nPost the metadata 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":21.205364,"sedDocuments":[{"location":"BIOMD0000000199_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  BIOMD0000000199_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 37 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 15 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000199_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":20.804774,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":19.862164,"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":0.297521,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_FeIII","status":"SUCCEEDED"},{"id":"autogen_task1_FeII","status":"SUCCEEDED"},{"id":"autogen_task1_FeII_O2","status":"SUCCEEDED"},{"id":"autogen_task1_FeIII_star","status":"SUCCEEDED"},{"id":"autogen_task1_FeII_star","status":"SUCCEEDED"},{"id":"autogen_task1_FeII_star_O2","status":"SUCCEEDED"},{"id":"autogen_task1_FeIII_NO","status":"SUCCEEDED"},{"id":"autogen_task1_FeII_NO","status":"SUCCEEDED"},{"id":"autogen_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_task1_O2","status":"SUCCEEDED"},{"id":"autogen_task1_citrulline","status":"SUCCEEDED"},{"id":"autogen_task1_NO3","status":"SUCCEEDED"},{"id":"autogen_task1_NO","status":"SUCCEEDED"},{"id":"autogen_task1_NADPplus","status":"SUCCEEDED"},{"id":"autogen_task1_FeIII_t","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_cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_r1","status":"SUCCEEDED"},{"id":"autogen_task1_r2","status":"SUCCEEDED"},{"id":"autogen_task1_r3","status":"SUCCEEDED"},{"id":"autogen_task1_r4","status":"SUCCEEDED"},{"id":"autogen_task1_r5","status":"SUCCEEDED"},{"id":"autogen_task1_r6","status":"SUCCEEDED"},{"id":"autogen_task1_rF","status":"SUCCEEDED"},{"id":"autogen_task1_rG","status":"SUCCEEDED"},{"id":"autogen_task1_r9","status":"SUCCEEDED"},{"id":"autogen_task1_r10","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.493537,"curves":[{"id":"autogen_curve_task1_FeIII","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FeII","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FeII_O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FeIII_star","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FeII_star","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FeII_star_O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FeIII_NO","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FeII_NO","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_citrulline","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NO3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NO","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADPplus","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FeIII_t","status":"SUCCEEDED"}]}]}]}