{"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    452      0 --:--:-- --:--:-- --:--:--   452\n\r100  312k  100  312k    0     0   732k      0 --:--:-- --:--:-- --:--:--  732k\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 (18.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/rawLog.txt\nCompleted 5.1 KiB/5.1 KiB (55.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/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/reports.h5 (deflated 10%)\n  adding: outputs/BIOMD0000000232_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000232_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/271.8 KiB (5.7 MiB/s) with 1 file(s) remaining\rCompleted 271.8 KiB/271.8 KiB (2.7 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/outputs/reports.h5\nCompleted 256.0 KiB/280.9 KiB (5.6 MiB/s) with 4 file(s) remaining\rCompleted 256.9 KiB/280.9 KiB (2.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/output.zip\nCompleted 256.9 KiB/280.9 KiB (2.7 MiB/s) with 3 file(s) remaining\rCompleted 269.6 KiB/280.9 KiB (2.4 MiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000232_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/outputs/BIOMD0000000232_url.sedml/autogen_plot_for_task1.pdf\nCompleted 269.6 KiB/280.9 KiB (2.4 MiB/s) with 2 file(s) remaining\rCompleted 278.2 KiB/280.9 KiB (2.4 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/outputs/plots.zip\nCompleted 278.2 KiB/280.9 KiB (2.4 MiB/s) with 1 file(s) remaining\rCompleted 280.9 KiB/280.9 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000232-biopax2.owl  \n  inflating: contents/BIOMD0000000232-biopax3.owl  \n  inflating: contents/BIOMD0000000232-matlab.m  \n  inflating: contents/BIOMD0000000232-octave.m  \n  inflating: contents/BIOMD0000000232.m  \n  inflating: contents/BIOMD0000000232.ode  \n  inflating: contents/BIOMD0000000232.pdf  \n  inflating: contents/BIOMD0000000232.png  \n  inflating: contents/BIOMD0000000232.svg  \n  inflating: contents/BIOMD0000000232_url.sedml  \n  inflating: contents/BIOMD0000000232_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 50.8 KiB/586.4 KiB (585.3 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000232-biopax3.owl to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232-biopax3.owl\nCompleted 50.8 KiB/586.4 KiB (585.3 KiB/s) with 14 file(s) remaining\rCompleted 58.9 KiB/586.4 KiB (555.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000232-matlab.m to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232-matlab.m\nCompleted 58.9 KiB/586.4 KiB (555.5 KiB/s) with 13 file(s) remaining\rCompleted 94.5 KiB/586.4 KiB (695.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000232-biopax2.owl to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232-biopax2.owl\nCompleted 94.5 KiB/586.4 KiB (695.8 KiB/s) with 12 file(s) remaining\rCompleted 102.6 KiB/586.4 KiB (689.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000232-octave.m to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232-octave.m\nCompleted 102.6 KiB/586.4 KiB (689.1 KiB/s) with 11 file(s) remaining\rCompleted 105.0 KiB/586.4 KiB (697.9 KiB/s) with 11 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/metadata.rdf\nCompleted 105.0 KiB/586.4 KiB (697.9 KiB/s) with 10 file(s) remaining\rCompleted 132.7 KiB/586.4 KiB (832.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000232.svg to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232.svg\nCompleted 132.7 KiB/586.4 KiB (832.6 KiB/s) with 9 file(s) remaining\rCompleted 144.5 KiB/586.4 KiB (877.7 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/curation_image.png\nCompleted 144.5 KiB/586.4 KiB (877.7 KiB/s) with 8 file(s) remaining\rCompleted 186.0 KiB/586.4 KiB (1.1 MiB/s) with 8 file(s) remaining  \rupload: contents/BIOMD0000000232_url.xml to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232_url.xml\nCompleted 186.0 KiB/586.4 KiB (1.1 MiB/s) with 7 file(s) remaining\rCompleted 213.6 KiB/586.4 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000232_url.sedml to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232_url.sedml\nCompleted 213.6 KiB/586.4 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 214.0 KiB/586.4 KiB (1.2 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/curation_notes.txt\nCompleted 214.0 KiB/586.4 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 431.3 KiB/586.4 KiB (2.2 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000232.pdf to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232.pdf\nCompleted 431.3 KiB/586.4 KiB (2.2 MiB/s) with 4 file(s) remaining\rCompleted 433.0 KiB/586.4 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/manifest.xml\nCompleted 433.0 KiB/586.4 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 572.9 KiB/586.4 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000232.png to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232.png\nCompleted 572.9 KiB/586.4 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 581.0 KiB/586.4 KiB (2.7 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000232.m to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232.m\nCompleted 581.0 KiB/586.4 KiB (2.7 MiB/s) with 1 file(s) remaining\rCompleted 586.4 KiB/586.4 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000232.ode to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/contents/BIOMD0000000232.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (143.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109f549c0d898ffdde90c/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000232_url.sedml\ncreating dataset /BIOMD0000000232_url.sedml/autogen_plot_for_task1, shape: (15, 1001), type: float64\ndataset created, uuid: d-781e22aa-8e9b9c56-616e-9d19e0-556f14, chunk_size: (15, 1001)\ncreating dataset /BIOMD0000000232_url.sedml/autogen_report_for_task1, shape: (51, 1001), type: float64\ndataset created, uuid: d-781e22aa-8e9b9c56-e8dc-82c75e-2426c1, chunk_size: (51, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000232_url.sedml\ncreating attribute uri in /BIOMD0000000232_url.sedml\ncreating attribute _type in /BIOMD0000000232_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000232_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000232_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000232_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000232_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000232_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000232_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000232_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000232_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000232_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000232_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000232_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000232_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000232_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000232_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000232_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000232_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000232_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000232_url.sedml\ncreate_links: /BIOMD0000000232_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000232_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000232_url.sedml/autogen_plot_for_task1, shape: (15, 1001), type: float64\niterating over chunks for /BIOMD0000000232_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 15, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000232_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000232_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000232_url.sedml/autogen_report_for_task1, shape: (51, 1001), type: float64\niterating over chunks for /BIOMD0000000232_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 51, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000232_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647109f549c0d898ffdde90c\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 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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":23.391359,"sedDocuments":[{"location":"BIOMD0000000232_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  BIOMD0000000232_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 51 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 14 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000232_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":23.024517,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":21.970686,"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":0.425593,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_H","status":"SUCCEEDED"},{"id":"autogen_task1_He","status":"SUCCEEDED"},{"id":"autogen_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_task1_AcCoA","status":"SUCCEEDED"},{"id":"autogen_task1_KG","status":"SUCCEEDED"},{"id":"autogen_task1_Cit","status":"SUCCEEDED"},{"id":"autogen_task1_OAA","status":"SUCCEEDED"},{"id":"autogen_task1_O2","status":"SUCCEEDED"},{"id":"autogen_task1_iP","status":"SUCCEEDED"},{"id":"autogen_task1_Pyr","status":"SUCCEEDED"},{"id":"autogen_task1_H2O","status":"SUCCEEDED"},{"id":"autogen_task1_ATPcrit","status":"SUCCEEDED"},{"id":"autogen_task1_At","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_DeltaGtransport","status":"SUCCEEDED"},{"id":"autogen_task1_DeltaPsi","status":"SUCCEEDED"},{"id":"autogen_task1_DeltaPsim","status":"SUCCEEDED"},{"id":"autogen_task1_F","status":"SUCCEEDED"},{"id":"autogen_task1_JANT","status":"SUCCEEDED"},{"id":"autogen_task1_JATP","status":"SUCCEEDED"},{"id":"autogen_task1_Jleak","status":"SUCCEEDED"},{"id":"autogen_task1_Jresp","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_Kapp","status":"SUCCEEDED"},{"id":"autogen_task1_Nt","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_T","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_kANT","status":"SUCCEEDED"},{"id":"autogen_task1_kATP","status":"SUCCEEDED"},{"id":"autogen_task1_kleak","status":"SUCCEEDED"},{"id":"autogen_task1_kresp","status":"SUCCEEDED"},{"id":"autogen_task1_cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_mitochondrion","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"},{"id":"autogen_task1_v5","status":"SUCCEEDED"},{"id":"autogen_task1_v6","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"},{"id":"autogen_task1_v8","status":"SUCCEEDED"},{"id":"autogen_task1_vresp","status":"SUCCEEDED"},{"id":"autogen_task1_vATP","status":"SUCCEEDED"},{"id":"autogen_task1_vANT","status":"SUCCEEDED"},{"id":"autogen_task1_vleak","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.461377,"curves":[{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_H","status":"SUCCEEDED"},{"id":"autogen_curve_task1_He","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AcCoA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_KG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cit","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OAA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_O2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_iP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pyr","status":"SUCCEEDED"},{"id":"autogen_curve_task1_H2O","status":"SUCCEEDED"}]}]}]}