{"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    459      0 --:--:-- --:--:-- --:--:--   460\n\r100 76616  100 76616    0     0   179k      0 --:--:-- --:--:-- --:--:--  179k\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 (26.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/rawLog.txt\nCompleted 3.3 KiB/3.3 KiB (44.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/ (stored 0%)\n  adding: outputs/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/plot_1_task1.pdf (deflated 30%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/reports.h5 (deflated 24%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 88.7 KiB/88.7 KiB (826.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/outputs/reports.h5\nCompleted 80.1 KiB/107.1 KiB (815.9 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/output.zip\nCompleted 80.1 KiB/107.1 KiB (815.9 KiB/s) with 3 file(s) remaining\rCompleted 94.5 KiB/107.1 KiB (814.8 KiB/s) with 3 file(s) remaining\rupload: outputs/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/outputs/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/plot_1_task1.pdf\nCompleted 94.5 KiB/107.1 KiB (814.8 KiB/s) with 2 file(s) remaining\rCompleted 104.3 KiB/107.1 KiB (851.6 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/outputs/plots.zip\nCompleted 104.3 KiB/107.1 KiB (851.6 KiB/s) with 1 file(s) remaining\rCompleted 107.1 KiB/107.1 KiB (862.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Fig 1.png      \n  inflating: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy-biopax2.owl  \n  inflating: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy-biopax3.owl  \n  inflating: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy-matlab.m  \n  inflating: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy-octave.m  \n  inflating: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.cps  \n  inflating: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.ode  \n  inflating: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml  \n  inflating: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 11.1 KiB/216.3 KiB (179.8 KiB/s) with 13 file(s) remaining\rupload: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy-biopax2.owl\nCompleted 11.1 KiB/216.3 KiB (179.8 KiB/s) with 12 file(s) remaining\rCompleted 14.8 KiB/216.3 KiB (117.4 KiB/s) with 12 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/contents/metadata.rdf\nCompleted 14.8 KiB/216.3 KiB (117.4 KiB/s) with 11 file(s) remaining\rCompleted 19.7 KiB/216.3 KiB (154.3 KiB/s) with 11 file(s) remaining\rupload: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy-matlab.m to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy-matlab.m\nCompleted 19.7 KiB/216.3 KiB (154.3 KiB/s) with 10 file(s) remaining\rCompleted 35.0 KiB/216.3 KiB (269.8 KiB/s) with 10 file(s) remaining\rupload: contents/Yazdjer2019 - 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reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml\nCompleted 155.4 KiB/216.3 KiB (780.1 KiB/s) with 2 file(s) remaining\rCompleted 216.2 KiB/216.3 KiB (1.0 MiB/s) with 2 file(s) remaining  \rupload: contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.cps to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/contents/Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.cps\nCompleted 216.2 KiB/216.3 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 216.3 KiB/216.3 KiB (915.3 KiB/s) with 1 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/contents/curation_notes.txt\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 10.0 KiB/10.0 KiB (132.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6877b666965506128f/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml\ncreating dataset /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\ndataset created, uuid: d-fd6ae1b7-8753cf5c-4615-01c6d4-8ed9fa, chunk_size: (20, 1001)\ncreating dataset /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/plot_1_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-fd6ae1b7-8753cf5c-c9e9-e7131b-4441e6, chunk_size: (4, 1001)\ncreating attribute combineArchiveLocation in /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml\ncreating attribute uri in /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml\ncreating attribute _type in /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Yazdjer2019 - 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reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\niterating over chunks for /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 1001, 1))\ndone with dataload for /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/autogen_report_for_task1\nwrite_dataset src: /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/plot_1_task1 to tgt: /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/plot_1_task1, shape: (4, 1001), type: float64\niterating over chunks for /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b6877b666965506128f\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 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.\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":1.275205,"sedDocuments":[{"location":"Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.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  Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 20 data sets\r\n    Plots (1):\r\n      plot_1_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: Yazdjer2019 - reinforcement learning-based control of tumor growth under anti-angiogenic therapy.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":0.865792,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.131714,"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":10000,"Relative Tolerance":0.000001}}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.418743,"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":0.213668,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_volume_x_1","status":"SUCCEEDED"},{"id":"autogen_task1_endothelial_volume_x_2","status":"SUCCEEDED"},{"id":"autogen_task1_concentration_of_administrated_inhibitor_x_3","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_1","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_2","status":"SUCCEEDED"},{"id":"autogen_task1_lambda_3","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_e","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_tumor_growth","status":"SUCCEEDED"},{"id":"autogen_task1_endothelial_loss","status":"SUCCEEDED"},{"id":"autogen_task1_stimulatory_effect","status":"SUCCEEDED"},{"id":"autogen_task1_inhibition_effect","status":"SUCCEEDED"},{"id":"autogen_task1_drug_kill","status":"SUCCEEDED"},{"id":"autogen_task1_inhibitor_clearance","status":"SUCCEEDED"},{"id":"autogen_task1_administrated_inhibitor","status":"SUCCEEDED"}]}]}]}