{"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    440      0 --:--:-- --:--:-- --:--:--   441\n\r 31  251k   31 82060    0     0   179k      0  0:00:01 --:--:--  0:00:01  179k\r100  251k  100  251k    0     0   550k      0 --:--:-- --:--:-- --:--:-- 16.7M\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 (20.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (35.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/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/BIOMD0000000390_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000390_url.sedml/autogen_plot_for_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 190.3 KiB/190.3 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/outputs/reports.h5\nCompleted 10.6 KiB/208.5 KiB (93.2 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/outputs/plots.zip\nCompleted 10.6 KiB/208.5 KiB (93.2 KiB/s) with 3 file(s) remaining\rCompleted 25.3 KiB/208.5 KiB (206.7 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000390_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/outputs/BIOMD0000000390_url.sedml/autogen_plot_for_task1.pdf\nCompleted 25.3 KiB/208.5 KiB (206.7 KiB/s) with 2 file(s) remaining\rCompleted 205.8 KiB/208.5 KiB (1.5 MiB/s) with 2 file(s) remaining \rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/output.zip\nCompleted 205.8 KiB/208.5 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 208.5 KiB/208.5 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000390-biopax2.owl  \n  inflating: contents/BIOMD0000000390-biopax3.owl  \n  inflating: contents/BIOMD0000000390-matlab.m  \n  inflating: contents/BIOMD0000000390-octave.m  \n  inflating: contents/BIOMD0000000390.m  \n  inflating: contents/BIOMD0000000390.ode  \n  inflating: contents/BIOMD0000000390.pdf  \n  inflating: contents/BIOMD0000000390.png  \n  inflating: contents/BIOMD0000000390.svg  \n  inflating: contents/BIOMD0000000390_url.sedml  \n  inflating: contents/BIOMD0000000390_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 15.9 KiB/428.4 KiB (205.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000390-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390-biopax2.owl\nCompleted 15.9 KiB/428.4 KiB (205.0 KiB/s) with 14 file(s) remaining\rCompleted 22.6 KiB/428.4 KiB (178.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000390-matlab.m to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390-matlab.m\nCompleted 22.6 KiB/428.4 KiB (178.7 KiB/s) with 13 file(s) remaining\rCompleted 29.3 KiB/428.4 KiB (184.1 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000390-octave.m to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390-octave.m\nCompleted 29.3 KiB/428.4 KiB (184.1 KiB/s) with 12 file(s) remaining\rCompleted 60.2 KiB/428.4 KiB (360.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000390_url.xml to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390_url.xml\nCompleted 60.2 KiB/428.4 KiB (360.9 KiB/s) with 11 file(s) remaining\rCompleted 73.7 KiB/428.4 KiB (433.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000390_url.sedml to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390_url.sedml\nCompleted 73.7 KiB/428.4 KiB (433.7 KiB/s) with 10 file(s) remaining\rCompleted 137.7 KiB/428.4 KiB (770.9 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000390.png to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390.png\nCompleted 137.7 KiB/428.4 KiB (770.9 KiB/s) with 9 file(s) remaining\rCompleted 138.0 KiB/428.4 KiB (750.9 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/curation_notes.txt\nCompleted 138.0 KiB/428.4 KiB (750.9 KiB/s) with 8 file(s) remaining\rCompleted 142.0 KiB/428.4 KiB (757.7 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/metadata.rdf\nCompleted 142.0 KiB/428.4 KiB (757.7 KiB/s) with 7 file(s) remaining\rCompleted 160.0 KiB/428.4 KiB (840.4 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000390.svg to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390.svg\nCompleted 160.0 KiB/428.4 KiB (840.4 KiB/s) with 6 file(s) remaining\rCompleted 161.7 KiB/428.4 KiB (835.2 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/manifest.xml\nCompleted 161.7 KiB/428.4 KiB (835.2 KiB/s) with 5 file(s) remaining\rCompleted 352.9 KiB/428.4 KiB (1.6 MiB/s) with 5 file(s) remaining  \rupload: contents/BIOMD0000000390.pdf to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390.pdf\nCompleted 352.9 KiB/428.4 KiB (1.6 MiB/s) with 4 file(s) remaining\rCompleted 392.4 KiB/428.4 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/curation_image.png\nCompleted 392.4 KiB/428.4 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 399.1 KiB/428.4 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000390.m to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390.m\nCompleted 399.1 KiB/428.4 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 423.8 KiB/428.4 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000390-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390-biopax3.owl\nCompleted 423.8 KiB/428.4 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 428.4 KiB/428.4 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000390.ode to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/contents/BIOMD0000000390.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (80.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b1e77b6669655060ce7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000390_url.sedml\ncreating dataset /BIOMD0000000390_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-6db2e4d2-c9a8224b-6eea-71e38a-cf052c, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000390_url.sedml/autogen_report_for_task1, shape: (22, 1001), type: float64\ndataset created, uuid: d-6db2e4d2-c9a8224b-6199-96d954-553fc7, chunk_size: (22, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000390_url.sedml\ncreating attribute uri in /BIOMD0000000390_url.sedml\ncreating attribute _type in /BIOMD0000000390_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000390_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000390_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000390_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000390_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000390_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000390_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000390_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000390_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000390_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000390_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000390_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000390_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000390_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000390_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000390_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000390_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000390_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000390_url.sedml\ncreate_links: /BIOMD0000000390_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000390_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000390_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000390_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000390_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000390_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000390_url.sedml/autogen_report_for_task1, shape: (22, 1001), type: float64\niterating over chunks for /BIOMD0000000390_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 22, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000390_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b1e77b6669655060ce7\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 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":1.548056,"sedDocuments":[{"location":"BIOMD0000000390_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  BIOMD0000000390_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 22 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000390_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":1.130664,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.219978,"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":0.199729,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_RuBP","status":"SUCCEEDED"},{"id":"autogen_task1_PGA","status":"SUCCEEDED"},{"id":"autogen_task1_TP","status":"SUCCEEDED"},{"id":"autogen_task1_Ru5P","status":"SUCCEEDED"},{"id":"autogen_task1_Pi","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_E_RuBisCO","status":"SUCCEEDED"},{"id":"autogen_task1_totRuBP","status":"SUCCEEDED"},{"id":"autogen_task1_TPc","status":"SUCCEEDED"},{"id":"autogen_task1_Pic","status":"SUCCEEDED"},{"id":"autogen_task1_V6","status":"SUCCEEDED"},{"id":"autogen_task1_P_0","status":"SUCCEEDED"},{"id":"autogen_task1_chloroplast","status":"SUCCEEDED"},{"id":"autogen_task1_cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_RuBisCO","status":"SUCCEEDED"},{"id":"autogen_task1_PGA_red","status":"SUCCEEDED"},{"id":"autogen_task1_TP_red","status":"SUCCEEDED"},{"id":"autogen_task1_RuBP_reg","status":"SUCCEEDED"},{"id":"autogen_task1_TPT","status":"SUCCEEDED"},{"id":"autogen_task1_ATP_S","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.565112,"curves":[{"id":"autogen_curve_task1_RuBP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PGA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_TP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ru5P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E_RuBisCO","status":"SUCCEEDED"},{"id":"autogen_curve_task1_totRuBP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_TPc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pic","status":"SUCCEEDED"}]}]}]}