{"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    386      0 --:--:-- --:--:-- --:--:--   387\n\r100  722k  100  722k    0     0  1466k      0 --:--:-- --:--:-- --:--:-- 1466k\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 (20.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/rawLog.txt\nCompleted 5.3 KiB/5.3 KiB (75.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/BIOMD0000000391_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000391_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 16%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 157.8 KiB/157.8 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/outputs/reports.h5\nCompleted 145.6 KiB/171.9 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/output.zip\nCompleted 145.6 KiB/171.9 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 159.5 KiB/171.9 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000391_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/outputs/BIOMD0000000391_url.sedml/autogen_plot_for_task1.pdf\nCompleted 159.5 KiB/171.9 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 169.3 KiB/171.9 KiB (1.3 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/outputs/plots.zip\nCompleted 169.3 KiB/171.9 KiB (1.3 MiB/s) with 1 file(s) remaining\rCompleted 171.9 KiB/171.9 KiB (1.3 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000391-biopax2.owl  \n  inflating: contents/BIOMD0000000391-biopax3.owl  \n  inflating: contents/BIOMD0000000391-matlab.m  \n  inflating: contents/BIOMD0000000391-octave.m  \n  inflating: contents/BIOMD0000000391.m  \n  inflating: contents/BIOMD0000000391.ode  \n  inflating: contents/BIOMD0000000391.pdf  \n  inflating: contents/BIOMD0000000391.png  \n  inflating: contents/BIOMD0000000391.svg  \n  inflating: contents/BIOMD0000000391_url.sedml  \n  inflating: contents/BIOMD0000000391_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 59.8 KiB/1.2 MiB (731.8 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000391-biopax3.owl to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391-biopax3.owl\nCompleted 59.8 KiB/1.2 MiB (731.8 KiB/s) with 14 file(s) remaining\rCompleted 75.6 KiB/1.2 MiB (506.8 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000391-octave.m to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391-octave.m\nCompleted 75.6 KiB/1.2 MiB (506.8 KiB/s) with 13 file(s) remaining\rCompleted 102.4 KiB/1.2 MiB (673.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000391_url.sedml to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391_url.sedml\nCompleted 102.4 KiB/1.2 MiB (673.5 KiB/s) with 12 file(s) remaining\rCompleted 118.3 KiB/1.2 MiB (765.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000391-matlab.m to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391-matlab.m\nCompleted 118.3 KiB/1.2 MiB (765.7 KiB/s) with 11 file(s) remaining\rCompleted 181.4 KiB/1.2 MiB (1.1 MiB/s) with 11 file(s) remaining  \rupload: contents/BIOMD0000000391.svg to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391.svg\nCompleted 181.4 KiB/1.2 MiB (1.1 MiB/s) with 10 file(s) remaining\rCompleted 219.0 KiB/1.2 MiB (1.3 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000391-biopax2.owl to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391-biopax2.owl\nCompleted 219.0 KiB/1.2 MiB (1.3 MiB/s) with 9 file(s) remaining\rCompleted 222.7 KiB/1.2 MiB (1.3 MiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/metadata.rdf\nCompleted 222.7 KiB/1.2 MiB (1.3 MiB/s) with 8 file(s) remaining\rCompleted 223.0 KiB/1.2 MiB (1.2 MiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/curation_notes.txt\nCompleted 223.0 KiB/1.2 MiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 291.6 KiB/1.2 MiB (1.5 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/curation_image.png\nCompleted 291.6 KiB/1.2 MiB (1.5 MiB/s) with 6 file(s) remaining\rCompleted 293.4 KiB/1.2 MiB (1.5 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/manifest.xml\nCompleted 293.4 KiB/1.2 MiB (1.5 MiB/s) with 5 file(s) remaining\rCompleted 361.5 KiB/1.2 MiB (1.9 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000391_url.xml to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391_url.xml\nCompleted 361.5 KiB/1.2 MiB (1.9 MiB/s) with 4 file(s) remaining\rCompleted 617.5 KiB/1.2 MiB (3.1 MiB/s) with 4 file(s) remaining\rCompleted 873.5 KiB/1.2 MiB (4.3 MiB/s) with 4 file(s) remaining\rCompleted 1.1 MiB/1.2 MiB (5.4 MiB/s) with 4 file(s) remaining  \rCompleted 1.1 MiB/1.2 MiB (5.1 MiB/s) with 4 file(s) remaining  \rupload: contents/BIOMD0000000391.ode to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391.ode\nCompleted 1.1 MiB/1.2 MiB (5.1 MiB/s) with 3 file(s) remaining\rCompleted 1.1 MiB/1.2 MiB (4.8 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000391.m to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391.m\nCompleted 1.1 MiB/1.2 MiB (4.8 MiB/s) with 2 file(s) remaining\rCompleted 1.2 MiB/1.2 MiB (4.7 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000391.pdf to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391.pdf\nCompleted 1.2 MiB/1.2 MiB (4.7 MiB/s) with 1 file(s) remaining\rCompleted 1.2 MiB/1.2 MiB (4.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000391.png to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/contents/BIOMD0000000391.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (131.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c4e5321246e8866daf3b/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000391_url.sedml\ncreating dataset /BIOMD0000000391_url.sedml/autogen_plot_for_task1, shape: (23, 1001), type: float64\ndataset created, uuid: d-c4e262a5-62d787d3-7c61-da32a4-ab3ca9, chunk_size: (23, 1001)\ncreating dataset /BIOMD0000000391_url.sedml/autogen_report_for_task1, shape: (46, 1001), type: float64\ndataset created, uuid: d-c4e262a5-62d787d3-6377-4a3d59-5be1e9, chunk_size: (46, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000391_url.sedml\ncreating attribute uri in /BIOMD0000000391_url.sedml\ncreating attribute _type in /BIOMD0000000391_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000391_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000391_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000391_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000391_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000391_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000391_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000391_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000391_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000391_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000391_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000391_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000391_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000391_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000391_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000391_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000391_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000391_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000391_url.sedml\ncreate_links: /BIOMD0000000391_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000391_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000391_url.sedml/autogen_plot_for_task1, shape: (23, 1001), type: float64\niterating over chunks for /BIOMD0000000391_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 23, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000391_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000391_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000391_url.sedml/autogen_report_for_task1, shape: (46, 1001), type: float64\niterating over chunks for /BIOMD0000000391_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 46, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000391_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c4e5321246e8866daf3b\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 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 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":30.972679,"sedDocuments":[{"location":"BIOMD0000000391_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  BIOMD0000000391_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 46 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 22 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000391_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":30.560644,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":29.33807,"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":0.40284,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_RuBP","status":"SUCCEEDED"},{"id":"autogen_task1_PGA","status":"SUCCEEDED"},{"id":"autogen_task1_DPGA","status":"SUCCEEDED"},{"id":"autogen_task1_GAP","status":"SUCCEEDED"},{"id":"autogen_task1_DHAP","status":"SUCCEEDED"},{"id":"autogen_task1_FBP","status":"SUCCEEDED"},{"id":"autogen_task1_F6P","status":"SUCCEEDED"},{"id":"autogen_task1_E4P","status":"SUCCEEDED"},{"id":"autogen_task1_SBP","status":"SUCCEEDED"},{"id":"autogen_task1_S7P","status":"SUCCEEDED"},{"id":"autogen_task1_X5P","status":"SUCCEEDED"},{"id":"autogen_task1_R5P","status":"SUCCEEDED"},{"id":"autogen_task1_Ru5P","status":"SUCCEEDED"},{"id":"autogen_task1_G6P","status":"SUCCEEDED"},{"id":"autogen_task1_G1P","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_task1_NADP","status":"SUCCEEDED"},{"id":"autogen_task1_H","status":"SUCCEEDED"},{"id":"autogen_task1_Pi","status":"SUCCEEDED"},{"id":"autogen_task1_Pext","status":"SUCCEEDED"},{"id":"autogen_task1_chloroplast","status":"SUCCEEDED"},{"id":"autogen_task1_cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_RuBisCO","status":"SUCCEEDED"},{"id":"autogen_task1_PGA_K","status":"SUCCEEDED"},{"id":"autogen_task1_GAP_DH","status":"SUCCEEDED"},{"id":"autogen_task1_TP_I","status":"SUCCEEDED"},{"id":"autogen_task1_FBP_A","status":"SUCCEEDED"},{"id":"autogen_task1_FBPase","status":"SUCCEEDED"},{"id":"autogen_task1_F6P_TK","status":"SUCCEEDED"},{"id":"autogen_task1_SBP_A","status":"SUCCEEDED"},{"id":"autogen_task1_SBPase","status":"SUCCEEDED"},{"id":"autogen_task1_S7P_TK","status":"SUCCEEDED"},{"id":"autogen_task1_R5P_I","status":"SUCCEEDED"},{"id":"autogen_task1_Ru5P_E","status":"SUCCEEDED"},{"id":"autogen_task1_Ru5P_K","status":"SUCCEEDED"},{"id":"autogen_task1_PG_I","status":"SUCCEEDED"},{"id":"autogen_task1_PG_M","status":"SUCCEEDED"},{"id":"autogen_task1_Starch_S","status":"SUCCEEDED"},{"id":"autogen_task1_Starch_P","status":"SUCCEEDED"},{"id":"autogen_task1_ATP_S","status":"SUCCEEDED"},{"id":"autogen_task1_TPT_PGA","status":"SUCCEEDED"},{"id":"autogen_task1_TPT_GAP","status":"SUCCEEDED"},{"id":"autogen_task1_TPT_DHAP","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.624543,"curves":[{"id":"autogen_curve_task1_RuBP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PGA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DPGA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DHAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FBP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_F6P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E4P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_SBP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S7P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X5P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R5P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ru5P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G6P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G1P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_H","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pext","status":"SUCCEEDED"}]}]}]}