{"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    431      0 --:--:-- --:--:-- --:--:--   433\n\r100 51823  100 51823    0     0   116k      0 --:--:-- --:--:-- --:--:--  116k\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 (20.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/rawLog.txt\nCompleted 3.1 KiB/3.1 KiB (27.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/Alharbi2019 TNVM - Fig11.sedml/ (stored 0%)\n  adding: outputs/Alharbi2019 TNVM - Fig11.sedml/plot_1_task1.pdf (deflated 27%)\n  adding: outputs/reports.h5 (deflated 20%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 105.8 KiB/105.8 KiB (836.4 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/outputs/reports.h5\nCompleted 95.9 KiB/119.7 KiB (1005.4 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/output.zip\nCompleted 95.9 KiB/119.7 KiB (1005.4 KiB/s) with 3 file(s) remaining\rCompleted 98.5 KiB/119.7 KiB (812.3 KiB/s) with 3 file(s) remaining \rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/rawLog.txt\nCompleted 98.5 KiB/119.7 KiB (812.3 KiB/s) with 2 file(s) remaining\rCompleted 107.3 KiB/119.7 KiB (868.3 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/outputs/plots.zip\nCompleted 107.3 KiB/119.7 KiB (868.3 KiB/s) with 1 file(s) remaining\rCompleted 119.7 KiB/119.7 KiB (856.0 KiB/s) with 1 file(s) remaining\rupload: outputs/Alharbi2019 TNVM - Fig11.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/outputs/Alharbi2019 TNVM - Fig11.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Alharbi2019 TNVM - Fig11.sedml  \n  inflating: contents/Alharbi2019 TNVM-biopax2.owl  \n  inflating: contents/Alharbi2019 TNVM-biopax3.owl  \n  inflating: contents/Alharbi2019 TNVM-matlab.m  \n  inflating: contents/Alharbi2019 TNVM-octave.m  \n  inflating: contents/Alharbi2019 TNVM.cps  \n  inflating: contents/Alharbi2019 TNVM.ode  \n  inflating: contents/Alharbi2019 TNVM.xml  \n  inflating: contents/Fig11.png      \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 13.2 KiB/186.4 KiB (178.0 KiB/s) with 13 file(s) remaining\rupload: contents/Alharbi2019 TNVM - Fig11.sedml to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/Alharbi2019 TNVM - Fig11.sedml\nCompleted 13.2 KiB/186.4 KiB (178.0 KiB/s) with 12 file(s) remaining\rCompleted 28.4 KiB/186.4 KiB (227.0 KiB/s) with 12 file(s) remaining\rupload: contents/Alharbi2019 TNVM-biopax3.owl to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/Alharbi2019 TNVM-biopax3.owl\nCompleted 28.4 KiB/186.4 KiB (227.0 KiB/s) with 11 file(s) remaining\rCompleted 41.7 KiB/186.4 KiB (297.1 KiB/s) with 11 file(s) remaining\rupload: contents/Fig11.png to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/Fig11.png\nCompleted 41.7 KiB/186.4 KiB (297.1 KiB/s) with 10 file(s) remaining\rCompleted 76.0 KiB/186.4 KiB (531.8 KiB/s) with 10 file(s) remaining\rupload: contents/Alharbi2019 TNVM.xml to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/Alharbi2019 TNVM.xml\nCompleted 76.0 KiB/186.4 KiB (531.8 KiB/s) with 9 file(s) remaining\rCompleted 143.0 KiB/186.4 KiB (928.2 KiB/s) with 9 file(s) remaining\rupload: contents/Alharbi2019 TNVM.cps to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/Alharbi2019 TNVM.cps\nCompleted 143.0 KiB/186.4 KiB (928.2 KiB/s) with 8 file(s) remaining\rCompleted 156.3 KiB/186.4 KiB (996.1 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/curation_image.png\nCompleted 156.3 KiB/186.4 KiB (996.1 KiB/s) with 7 file(s) remaining\rCompleted 161.0 KiB/186.4 KiB (1010.5 KiB/s) with 7 file(s) remaining\rupload: contents/Alharbi2019 TNVM-matlab.m to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/Alharbi2019 TNVM-matlab.m\nCompleted 161.0 KiB/186.4 KiB (1010.5 KiB/s) with 6 file(s) remaining\rCompleted 161.3 KiB/186.4 KiB (964.4 KiB/s) with 6 file(s) remaining \rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/curation_notes.txt\nCompleted 161.3 KiB/186.4 KiB (964.4 KiB/s) with 5 file(s) remaining\rCompleted 165.3 KiB/186.4 KiB (893.2 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/metadata.rdf\nCompleted 165.3 KiB/186.4 KiB (893.2 KiB/s) with 4 file(s) remaining\rCompleted 168.5 KiB/186.4 KiB (894.3 KiB/s) with 4 file(s) remaining\rupload: contents/Alharbi2019 TNVM.ode to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/Alharbi2019 TNVM.ode\nCompleted 168.5 KiB/186.4 KiB (894.3 KiB/s) with 3 file(s) remaining\rCompleted 180.3 KiB/186.4 KiB (905.6 KiB/s) with 3 file(s) remaining\rupload: contents/Alharbi2019 TNVM-biopax2.owl to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/Alharbi2019 TNVM-biopax2.owl\nCompleted 180.3 KiB/186.4 KiB (905.6 KiB/s) with 2 file(s) remaining\rCompleted 181.8 KiB/186.4 KiB (891.1 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/manifest.xml\nCompleted 181.8 KiB/186.4 KiB (891.1 KiB/s) with 1 file(s) remaining\rCompleted 186.4 KiB/186.4 KiB (838.5 KiB/s) with 1 file(s) remaining\rupload: contents/Alharbi2019 TNVM-octave.m to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/contents/Alharbi2019 TNVM-octave.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 7.9 KiB/7.9 KiB (83.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a61a077b6669655064b90/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Alharbi2019 TNVM - Fig11.sedml\ncreating dataset /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1, shape: (21, 1001), type: float64\ndataset created, uuid: d-de4a65f7-776fb46c-77e3-5275bb-6060d7, chunk_size: (21, 1001)\ncreating dataset /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-de4a65f7-776fb46c-60b7-e4fb5c-c4f11f, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /Alharbi2019 TNVM - Fig11.sedml\ncreating attribute uri in /Alharbi2019 TNVM - Fig11.sedml\ncreating attribute _type in /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\ncreating attribute uri in /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\ncreating attribute _type in /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\ncreating attribute sedmlId in /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\ncreating attribute sedmlName in /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\ncreating attribute uri in /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\ncreate_links: /\ngot link: Alharbi2019 TNVM - Fig11.sedml\ncreate_links: /Alharbi2019 TNVM - Fig11.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1 to tgt: /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1, shape: (21, 1001), type: float64\niterating over chunks for /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 21, 1), slice(0, 1001, 1))\ndone with dataload for /Alharbi2019 TNVM - Fig11.sedml/autogen_report_for_task1\nwrite_dataset src: /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1 to tgt: /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Alharbi2019 TNVM - Fig11.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a61a077b6669655064b90\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 the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.26267,"sedDocuments":[{"location":"Alharbi2019 TNVM - Fig11.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  Alharbi2019 TNVM - Fig11.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 21 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Alharbi2019 TNVM - Fig11.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_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: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":0.85366,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.125961,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters","value":{"Absolute Tolerance":1e-12,"Integrate Reduced Model":false,"Max Internal Steps":100000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.396031,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.208968,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cells","status":"SUCCEEDED"},{"id":"autogen_task1_Vitamins","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_beta1","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_alpha1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha2","status":"SUCCEEDED"},{"id":"autogen_task1_beta2","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_c1","status":"SUCCEEDED"},{"id":"autogen_task1_c2","status":"SUCCEEDED"},{"id":"autogen_task1_Whole_organism","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cell_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Normal_cell_death_inhibition","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cell_growth","status":"SUCCEEDED"},{"id":"autogen_task1_Tumor_cell_inhibition","status":"SUCCEEDED"},{"id":"autogen_task1_Vitamin_intake","status":"SUCCEEDED"},{"id":"autogen_task1_Vitamin_decay","status":"SUCCEEDED"}]}]}]}