{"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    434      0 --:--:-- --:--:-- --:--:--   435\n\r100 54743  100 54743    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 4 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 4\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 (4):\n    Succeeded: 4\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (14.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (41.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/Evans2005.sedml/ (stored 0%)\n  adding: outputs/Evans2005.sedml/plot_3_task1.pdf (deflated 32%)\n  adding: outputs/Evans2005.sedml/plot_2_task1.pdf (deflated 32%)\n  adding: outputs/Evans2005.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 55%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 75.2 KiB/75.2 KiB (833.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/outputs/reports.h5\nCompleted 65.2 KiB/136.9 KiB (571.3 KiB/s) with 6 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/output.zip\nCompleted 65.2 KiB/136.9 KiB (571.3 KiB/s) with 5 file(s) remaining\rCompleted 79.6 KiB/136.9 KiB (600.3 KiB/s) with 5 file(s) remaining\rupload: outputs/Evans2005.sedml/plot_3_task1.pdf to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/outputs/Evans2005.sedml/plot_3_task1.pdf\nCompleted 79.6 KiB/136.9 KiB (600.3 KiB/s) with 4 file(s) remaining\rCompleted 92.3 KiB/136.9 KiB (685.0 KiB/s) with 4 file(s) remaining\rupload: outputs/Evans2005.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/outputs/Evans2005.sedml/plot_1_task1.pdf\nCompleted 92.3 KiB/136.9 KiB (685.0 KiB/s) with 3 file(s) remaining\rCompleted 119.5 KiB/136.9 KiB (858.1 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/outputs/plots.zip\nCompleted 119.5 KiB/136.9 KiB (858.1 KiB/s) with 2 file(s) remaining\rCompleted 122.2 KiB/136.9 KiB (853.6 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/rawLog.txt\nCompleted 122.2 KiB/136.9 KiB (853.6 KiB/s) with 1 file(s) remaining\rCompleted 136.9 KiB/136.9 KiB (791.9 KiB/s) with 1 file(s) remaining\rupload: outputs/Evans2005.sedml/plot_2_task1.pdf to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/outputs/Evans2005.sedml/plot_2_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/Evans2005.sedml  \n  inflating: contents/Lee2017_Paracetamol_Metabolism-biopax2.owl  \n  inflating: contents/Lee2017_Paracetamol_Metabolism-biopax3.owl  \n  inflating: contents/Lee2017_Paracetamol_Metabolism-matlab.m  \n  inflating: contents/Lee2017_Paracetamol_Metabolism-octave.m  \n  inflating: contents/Lee2017_Paracetamol_Metabolism.cps  \n  inflating: contents/Lee2017_Paracetamol_Metabolism.ode  \n  inflating: contents/Lee2017_Paracetamol_Metabolism.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/figure.jpg     \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 7.6 KiB/210.3 KiB (90.1 KiB/s) with 13 file(s) remaining\rupload: contents/Lee2017_Paracetamol_Metabolism-biopax2.owl to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/Lee2017_Paracetamol_Metabolism-biopax2.owl\nCompleted 7.6 KiB/210.3 KiB (90.1 KiB/s) with 12 file(s) remaining\rCompleted 24.1 KiB/210.3 KiB (182.5 KiB/s) with 12 file(s) remaining\rupload: contents/Evans2005.sedml to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/Evans2005.sedml\nCompleted 24.1 KiB/210.3 KiB (182.5 KiB/s) with 11 file(s) remaining\rCompleted 32.6 KiB/210.3 KiB (222.0 KiB/s) with 11 file(s) remaining\rupload: contents/Lee2017_Paracetamol_Metabolism-biopax3.owl to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/Lee2017_Paracetamol_Metabolism-biopax3.owl\nCompleted 32.6 KiB/210.3 KiB (222.0 KiB/s) with 10 file(s) remaining\rCompleted 56.0 KiB/210.3 KiB (364.6 KiB/s) with 10 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/curation_image.jpeg\nCompleted 56.0 KiB/210.3 KiB (364.6 KiB/s) with 9 file(s) remaining\rCompleted 60.0 KiB/210.3 KiB (364.9 KiB/s) with 9 file(s) remaining\rupload: contents/Lee2017_Paracetamol_Metabolism.ode to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/Lee2017_Paracetamol_Metabolism.ode\nCompleted 60.0 KiB/210.3 KiB (364.9 KiB/s) with 8 file(s) remaining\rCompleted 66.5 KiB/210.3 KiB (397.9 KiB/s) with 8 file(s) remaining\rupload: contents/Lee2017_Paracetamol_Metabolism-matlab.m to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/Lee2017_Paracetamol_Metabolism-matlab.m\nCompleted 66.5 KiB/210.3 KiB (397.9 KiB/s) with 7 file(s) remaining\rCompleted 66.6 KiB/210.3 KiB (376.5 KiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/curation_notes.txt\nCompleted 66.6 KiB/210.3 KiB (376.5 KiB/s) with 6 file(s) remaining\rCompleted 67.9 KiB/210.3 KiB (377.7 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/metadata.rdf\nCompleted 67.9 KiB/210.3 KiB (377.7 KiB/s) with 5 file(s) remaining\rCompleted 69.5 KiB/210.3 KiB (363.5 KiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/manifest.xml\nCompleted 69.5 KiB/210.3 KiB (363.5 KiB/s) with 4 file(s) remaining\rCompleted 131.3 KiB/210.3 KiB (610.6 KiB/s) with 4 file(s) remaining\rupload: contents/Lee2017_Paracetamol_Metabolism.cps to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/Lee2017_Paracetamol_Metabolism.cps\nCompleted 131.3 KiB/210.3 KiB (610.6 KiB/s) with 3 file(s) remaining\rCompleted 154.6 KiB/210.3 KiB (704.7 KiB/s) with 3 file(s) remaining\rupload: contents/figure.jpg to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/figure.jpg\nCompleted 154.6 KiB/210.3 KiB (704.7 KiB/s) with 2 file(s) remaining\rCompleted 161.1 KiB/210.3 KiB (725.1 KiB/s) with 2 file(s) remaining\rupload: contents/Lee2017_Paracetamol_Metabolism-octave.m to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/Lee2017_Paracetamol_Metabolism-octave.m\nCompleted 161.1 KiB/210.3 KiB (725.1 KiB/s) with 1 file(s) remaining\rCompleted 210.3 KiB/210.3 KiB (769.3 KiB/s) with 1 file(s) remaining\rupload: contents/Lee2017_Paracetamol_Metabolism.xml to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/contents/Lee2017_Paracetamol_Metabolism.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (101.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a61990fb37cdb9ae76e96/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Evans2005.sedml\ncreating dataset /Evans2005.sedml/autogen_report_for_task1, shape: (25, 251), type: float64\ndataset created, uuid: d-d84e3e71-0032ee76-b4af-ebdd92-ea07ca, chunk_size: (25, 251)\ncreating dataset /Evans2005.sedml/plot_1_task1, shape: (3, 251), type: float64\ndataset created, uuid: d-d84e3e71-0032ee76-15fa-e8c1fe-90afe4, chunk_size: (3, 251)\ncreating dataset /Evans2005.sedml/plot_2_task1, shape: (3, 251), type: float64\ndataset created, uuid: d-d84e3e71-0032ee76-6e80-3286da-b72db5, chunk_size: (3, 251)\ncreating dataset /Evans2005.sedml/plot_3_task1, shape: (3, 251), type: float64\ndataset created, uuid: d-d84e3e71-0032ee76-81f1-fb7287-bac9b2, chunk_size: (3, 251)\ncreating attribute combineArchiveLocation in /Evans2005.sedml\ncreating attribute uri in /Evans2005.sedml\ncreating attribute _type in /Evans2005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Evans2005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Evans2005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Evans2005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Evans2005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Evans2005.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Evans2005.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Evans2005.sedml/autogen_report_for_task1\ncreating attribute uri in /Evans2005.sedml/autogen_report_for_task1\ncreating attribute _type in /Evans2005.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Evans2005.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Evans2005.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Evans2005.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Evans2005.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Evans2005.sedml/plot_1_task1\ncreating attribute sedmlId in /Evans2005.sedml/plot_1_task1\ncreating attribute sedmlName in /Evans2005.sedml/plot_1_task1\ncreating attribute uri in /Evans2005.sedml/plot_1_task1\ncreating attribute _type in /Evans2005.sedml/plot_2_task1\ncreating attribute sedmlDataSetDataTypes in /Evans2005.sedml/plot_2_task1\ncreating attribute sedmlDataSetIds in /Evans2005.sedml/plot_2_task1\ncreating attribute sedmlDataSetLabels in /Evans2005.sedml/plot_2_task1\ncreating attribute sedmlDataSetNames in /Evans2005.sedml/plot_2_task1\ncreating attribute sedmlDataSetShapes in /Evans2005.sedml/plot_2_task1\ncreating attribute sedmlId in /Evans2005.sedml/plot_2_task1\ncreating attribute sedmlName in /Evans2005.sedml/plot_2_task1\ncreating attribute uri in /Evans2005.sedml/plot_2_task1\ncreating attribute _type in /Evans2005.sedml/plot_3_task1\ncreating attribute sedmlDataSetDataTypes in /Evans2005.sedml/plot_3_task1\ncreating attribute sedmlDataSetIds in /Evans2005.sedml/plot_3_task1\ncreating attribute sedmlDataSetLabels in /Evans2005.sedml/plot_3_task1\ncreating attribute sedmlDataSetNames in /Evans2005.sedml/plot_3_task1\ncreating attribute sedmlDataSetShapes in /Evans2005.sedml/plot_3_task1\ncreating attribute sedmlId in /Evans2005.sedml/plot_3_task1\ncreating attribute sedmlName in /Evans2005.sedml/plot_3_task1\ncreating attribute uri in /Evans2005.sedml/plot_3_task1\ncreate_links: /\ngot link: Evans2005.sedml\ncreate_links: /Evans2005.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\ngot link: plot_2_task1\ngot link: plot_3_task1\nwrite_dataset src: /Evans2005.sedml/autogen_report_for_task1 to tgt: /Evans2005.sedml/autogen_report_for_task1, shape: (25, 251), type: float64\niterating over chunks for /Evans2005.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 25, 1), slice(0, 251, 1))\ndone with dataload for /Evans2005.sedml/autogen_report_for_task1\nwrite_dataset src: /Evans2005.sedml/plot_1_task1 to tgt: /Evans2005.sedml/plot_1_task1, shape: (3, 251), type: float64\niterating over chunks for /Evans2005.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 251, 1))\ndone with dataload for /Evans2005.sedml/plot_1_task1\nwrite_dataset src: /Evans2005.sedml/plot_2_task1 to tgt: /Evans2005.sedml/plot_2_task1, shape: (3, 251), type: float64\niterating over chunks for /Evans2005.sedml/plot_2_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 251, 1))\ndone with dataload for /Evans2005.sedml/plot_2_task1\nwrite_dataset src: /Evans2005.sedml/plot_3_task1 to tgt: /Evans2005.sedml/plot_3_task1, shape: (3, 251), type: float64\niterating over chunks for /Evans2005.sedml/plot_3_task1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 251, 1))\ndone with dataload for /Evans2005.sedml/plot_3_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a61990fb37cdb9ae76e96\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 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.\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":1.761941,"sedDocuments":[{"location":"Evans2005.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 3 plots:\r\n  Evans2005.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 25 data sets\r\n    Plots (3):\r\n      plot_1_task1: 2 curves\r\n      plot_2_task1: 2 curves\r\n      plot_3_task1: 2 curves\r\n\r\nExecuting SED-ML file 1: Evans2005.sedml ...\r\n  Found 1 tasks and 4 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot_1_task1`\r\n      `plot_2_task1`\r\n      `plot_3_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 4 outputs ...\r\n      Generating output 1: `plot_1_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_2_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 3: `plot_3_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 4: `autogen_report_for_task1` ...","duration":1.264465,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.250359,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"plot_1_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.363341,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"},{"id":"p1_curve_2_task1","status":"SUCCEEDED"}]},{"id":"plot_2_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.173123,"curves":[{"id":"p2_curve_1_task1","status":"SUCCEEDED"},{"id":"p2_curve_2_task1","status":"SUCCEEDED"}]},{"id":"plot_3_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.175411,"curves":[{"id":"p3_curve_1_task1","status":"SUCCEEDED"},{"id":"p3_curve_2_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.10009,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_C_para__Basolateral___HepG2_","status":"SUCCEEDED"},{"id":"autogen_task1_C_para_Apical","status":"SUCCEEDED"},{"id":"autogen_task1_C_glu__Basolateral___HepG2_","status":"SUCCEEDED"},{"id":"autogen_task1_C_glu_Apical","status":"SUCCEEDED"},{"id":"autogen_task1_C_sulf__Basolateral___HepG2_","status":"SUCCEEDED"},{"id":"autogen_task1_C_sulf_Apical","status":"SUCCEEDED"},{"id":"autogen_task1_C_para_Caco_2","status":"SUCCEEDED"},{"id":"autogen_task1_C_sulf_Caco_2","status":"SUCCEEDED"},{"id":"autogen_task1_C_glu_Caco_2","status":"SUCCEEDED"},{"id":"autogen_task1_P_para","status":"SUCCEEDED"},{"id":"autogen_task1_Ai","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_s_caco","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_g_caco","status":"SUCCEEDED"},{"id":"autogen_task1_V_api","status":"SUCCEEDED"},{"id":"autogen_task1_V_caco","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_s_HepG2","status":"SUCCEEDED"},{"id":"autogen_task1_V_basol","status":"SUCCEEDED"},{"id":"autogen_task1_P_sulf","status":"SUCCEEDED"},{"id":"autogen_task1_P_glu","status":"SUCCEEDED"},{"id":"autogen_task1_Mp_g_HepG2","status":"SUCCEEDED"},{"id":"autogen_task1_time_threshold","status":"SUCCEEDED"},{"id":"autogen_task1_Apical","status":"SUCCEEDED"},{"id":"autogen_task1_Caco_2","status":"SUCCEEDED"},{"id":"autogen_task1_Basolateral___HepG2","status":"SUCCEEDED"}]}]}]}