{"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    438      0 --:--:-- --:--:-- --:--:--   438\n\r100  218k  100  218k    0     0   496k      0 --:--:-- --:--:-- --:--:--  496k\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 (25.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (68.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/ (stored 0%)\n  adding: outputs/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 36%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 70.0 KiB/70.0 KiB (777.0 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/outputs/reports.h5\nCompleted 57.4 KiB/84.3 KiB (623.6 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/output.zip\nCompleted 57.4 KiB/84.3 KiB (623.6 KiB/s) with 3 file(s) remaining\rCompleted 60.2 KiB/84.3 KiB (584.5 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/rawLog.txt\nCompleted 60.2 KiB/84.3 KiB (584.5 KiB/s) with 2 file(s) remaining\rCompleted 69.9 KiB/84.3 KiB (618.1 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/outputs/plots.zip\nCompleted 69.9 KiB/84.3 KiB (618.1 KiB/s) with 1 file(s) remaining\rCompleted 84.3 KiB/84.3 KiB (641.5 KiB/s) with 1 file(s) remaining\rupload: outputs/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/outputs/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Fig 3.png      \n  inflating: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-biopax2.owl  \n  inflating: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-biopax3.owl  \n  inflating: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-matlab.m  \n  inflating: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-octave.m  \n  inflating: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.cps  \n  inflating: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.ode  \n  inflating: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml  \n  inflating: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 100.6 KiB/431.2 KiB (1.2 MiB/s) with 13 file(s) remaining\rupload: contents/Fig 3.png to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/Fig 3.png\nCompleted 100.6 KiB/431.2 KiB (1.2 MiB/s) with 12 file(s) remaining\rCompleted 107.8 KiB/431.2 KiB (985.1 KiB/s) with 12 file(s) remaining\rupload: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-matlab.m to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-matlab.m\nCompleted 107.8 KiB/431.2 KiB (985.1 KiB/s) with 11 file(s) remaining\rCompleted 137.8 KiB/431.2 KiB (1.2 MiB/s) with 11 file(s) remaining  \rupload: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-biopax3.owl\nCompleted 137.8 KiB/431.2 KiB (1.2 MiB/s) with 10 file(s) remaining\rCompleted 159.4 KiB/431.2 KiB (1.2 MiB/s) with 10 file(s) remaining\rupload: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml\nCompleted 159.4 KiB/431.2 KiB (1.2 MiB/s) with 9 file(s) remaining\rCompleted 164.9 KiB/431.2 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.ode to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.ode\nCompleted 164.9 KiB/431.2 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 165.0 KiB/431.2 KiB (1.0 MiB/s) with 8 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/curation_notes.txt\nCompleted 165.0 KiB/431.2 KiB (1.0 MiB/s) with 7 file(s) remaining\rCompleted 167.0 KiB/431.2 KiB (1.0 MiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/manifest.xml\nCompleted 167.0 KiB/431.2 KiB (1.0 MiB/s) with 6 file(s) remaining\rCompleted 174.3 KiB/431.2 KiB (1.0 MiB/s) with 6 file(s) remaining\rupload: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-octave.m to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-octave.m\nCompleted 174.3 KiB/431.2 KiB (1.0 MiB/s) with 5 file(s) remaining\rCompleted 230.1 KiB/431.2 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.xml to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.xml\nCompleted 230.1 KiB/431.2 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 249.0 KiB/431.2 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification-biopax2.owl\nCompleted 249.0 KiB/431.2 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 349.6 KiB/431.2 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/curation_image.png\nCompleted 349.6 KiB/431.2 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 427.8 KiB/431.2 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.cps to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.cps\nCompleted 427.8 KiB/431.2 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 431.2 KiB/431.2 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.5 KiB/9.5 KiB (136.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b6a77b66696550612b1/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml\ncreating dataset /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1, shape: (35, 201), type: float64\ndataset created, uuid: d-3659a1ea-f57f0d7d-867c-77d245-8640c6, chunk_size: (35, 201)\ncreating dataset /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1, shape: (11, 201), type: float64\ndataset created, uuid: d-3659a1ea-f57f0d7d-48f7-a972c4-3102ab, chunk_size: (11, 201)\ncreating attribute combineArchiveLocation in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml\ncreating attribute uri in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml\ncreating attribute _type in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\ncreating attribute uri in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\ncreating attribute _type in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\ncreating attribute sedmlId in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\ncreating attribute sedmlName in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\ncreating attribute uri in /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\ncreate_links: /\ngot link: Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml\ncreate_links: /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1 to tgt: /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1, shape: (35, 201), type: float64\niterating over chunks for /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 35, 1), slice(0, 201, 1))\ndone with dataload for /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/autogen_report_for_task1\nwrite_dataset src: /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1 to tgt: /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1, shape: (11, 201), type: float64\niterating over chunks for /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 201, 1))\ndone with dataload for /Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b6a77b66696550612b1\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 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.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":19.118825,"sedDocuments":[{"location":"Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.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  Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 35 data sets\r\n    Plots (1):\r\n      plot_1_task1: 10 curves\r\n\r\nExecuting SED-ML file 1: Ito2019 - gefitnib resistance of lung adenocarcinoma caused by MET amplification.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":18.776311,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":18.243432,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.262272,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"},{"id":"p1_curve_3_task1","status":"SUCCEEDED"},{"id":"p1_curve_4_task1","status":"SUCCEEDED"},{"id":"p1_curve_5_task1","status":"SUCCEEDED"},{"id":"p1_curve_6_task1","status":"SUCCEEDED"},{"id":"p1_curve_7_task1","status":"SUCCEEDED"},{"id":"p1_curve_8_task1","status":"SUCCEEDED"},{"id":"p1_curve_9_task1","status":"SUCCEEDED"},{"id":"p1_curve_10_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.106587,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_X_1_EGFR","status":"SUCCEEDED"},{"id":"autogen_task1_X_4_EGFR_EGFR","status":"SUCCEEDED"},{"id":"autogen_task1_X_2_ErbB3","status":"SUCCEEDED"},{"id":"autogen_task1_X_6_ErbB3_ErbB3","status":"SUCCEEDED"},{"id":"autogen_task1_X_5_EGFR_ErbB3","status":"SUCCEEDED"},{"id":"autogen_task1_X_3_MET","status":"SUCCEEDED"},{"id":"autogen_task1_X_7_MET_MET","status":"SUCCEEDED"},{"id":"autogen_task1_X_10_p_MET_MET","status":"SUCCEEDED"},{"id":"autogen_task1_X_8_p_EGFR_ErbB3","status":"SUCCEEDED"},{"id":"autogen_task1_X_9_p_ErbB3_ErbB3","status":"SUCCEEDED"},{"id":"autogen_task1_l_1","status":"SUCCEEDED"},{"id":"autogen_task1_k_1","status":"SUCCEEDED"},{"id":"autogen_task1_l_2","status":"SUCCEEDED"},{"id":"autogen_task1_k_2","status":"SUCCEEDED"},{"id":"autogen_task1_l_3","status":"SUCCEEDED"},{"id":"autogen_task1_l_4","status":"SUCCEEDED"},{"id":"autogen_task1_k_3","status":"SUCCEEDED"},{"id":"autogen_task1_k_4","status":"SUCCEEDED"},{"id":"autogen_task1_k_p1","status":"SUCCEEDED"},{"id":"autogen_task1_k_p2","status":"SUCCEEDED"},{"id":"autogen_task1_k_p3","status":"SUCCEEDED"},{"id":"autogen_task1_l_p1","status":"SUCCEEDED"},{"id":"autogen_task1_l_p2","status":"SUCCEEDED"},{"id":"autogen_task1_l_p3","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_EGFR_EGFR_formation","status":"SUCCEEDED"},{"id":"autogen_task1_ErbB3_ErbB3_formation","status":"SUCCEEDED"},{"id":"autogen_task1_EGFR_ErbB3_formation","status":"SUCCEEDED"},{"id":"autogen_task1_MET_MET_formation","status":"SUCCEEDED"},{"id":"autogen_task1_MET_MET_transformation","status":"SUCCEEDED"},{"id":"autogen_task1_phosphorylation_1","status":"SUCCEEDED"},{"id":"autogen_task1_phosphorylation_2","status":"SUCCEEDED"},{"id":"autogen_task1_gefitinib_1","status":"SUCCEEDED"},{"id":"autogen_task1_gefitnib_2","status":"SUCCEEDED"}]}]}]}