{"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    435      0 --:--:-- --:--:-- --:--:--   435\n\r100  187k  100  187k    0     0   435k      0 --:--:-- --:--:-- --:--:--  435k\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 (24.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/rawLog.txt\nCompleted 6.7 KiB/6.7 KiB (74.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 85%)\n  adding: outputs/Diedrichs2018.sedml/ (stored 0%)\n  adding: outputs/Diedrichs2018.sedml/plot_1_task1.pdf (deflated 20%)\n  adding: outputs/reports.h5 (deflated 7%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/416.6 KiB (5.5 MiB/s) with 1 file(s) remaining\rCompleted 416.6 KiB/416.6 KiB (3.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/outputs/reports.h5\nCompleted 256.0 KiB/448.6 KiB (3.5 MiB/s) with 4 file(s) remaining\rCompleted 273.2 KiB/448.6 KiB (3.6 MiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/outputs/plots.zip\nCompleted 273.2 KiB/448.6 KiB (3.6 MiB/s) with 3 file(s) remaining\rCompleted 295.0 KiB/448.6 KiB (2.6 MiB/s) with 3 file(s) remaining\rupload: outputs/Diedrichs2018.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/outputs/Diedrichs2018.sedml/plot_1_task1.pdf\nCompleted 295.0 KiB/448.6 KiB (2.6 MiB/s) with 2 file(s) remaining\rCompleted 445.9 KiB/448.6 KiB (3.4 MiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/output.zip\nCompleted 445.9 KiB/448.6 KiB (3.4 MiB/s) with 1 file(s) remaining\rCompleted 448.6 KiB/448.6 KiB (3.0 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000703-biopax2.owl  \n  inflating: contents/BIOMD0000000703-biopax3.owl  \n  inflating: contents/BIOMD0000000703-matlab.m  \n  inflating: contents/BIOMD0000000703-octave.m  \n  inflating: contents/BIOMD0000000703.m  \n  inflating: contents/BIOMD0000000703.ode  \n  inflating: contents/BIOMD0000000703.png  \n  inflating: contents/BIOMD0000000703.svg  \n  inflating: contents/BIOMD0000000703_url.xml  \n  inflating: contents/Diedrichs2018.cps  \n  inflating: contents/Diedrichs2018.sedml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 20.2 KiB/707.4 KiB (289.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000703-biopax2.owl to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/BIOMD0000000703-biopax2.owl\nCompleted 20.2 KiB/707.4 KiB (289.4 KiB/s) with 14 file(s) remaining\rCompleted 36.1 KiB/707.4 KiB (284.4 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000703.m to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/BIOMD0000000703.m\nCompleted 36.1 KiB/707.4 KiB (284.4 KiB/s) with 13 file(s) remaining\rCompleted 40.7 KiB/707.4 KiB (314.6 KiB/s) with 13 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/metadata.rdf\nCompleted 40.7 KiB/707.4 KiB (314.6 KiB/s) with 12 file(s) remaining\rCompleted 87.0 KiB/707.4 KiB (655.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000703.svg to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/BIOMD0000000703.svg\nCompleted 87.0 KiB/707.4 KiB (655.1 KiB/s) with 11 file(s) remaining\rCompleted 222.5 KiB/707.4 KiB (1.6 MiB/s) with 11 file(s) remaining \rupload: contents/BIOMD0000000703_url.xml to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/BIOMD0000000703_url.xml\nCompleted 222.5 KiB/707.4 KiB (1.6 MiB/s) with 10 file(s) remaining\rCompleted 334.8 KiB/707.4 KiB (2.3 MiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000703.png to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/BIOMD0000000703.png\nCompleted 334.8 KiB/707.4 KiB (2.3 MiB/s) with 9 file(s) remaining\rCompleted 375.2 KiB/707.4 KiB (2.3 MiB/s) with 9 file(s) remaining\rupload: contents/Diedrichs2018.sedml to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/Diedrichs2018.sedml\nCompleted 375.2 KiB/707.4 KiB (2.3 MiB/s) with 8 file(s) remaining\rCompleted 602.1 KiB/707.4 KiB (3.7 MiB/s) with 8 file(s) remaining\rupload: contents/Diedrichs2018.cps to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/Diedrichs2018.cps\nCompleted 602.1 KiB/707.4 KiB (3.7 MiB/s) with 7 file(s) remaining\rCompleted 602.7 KiB/707.4 KiB (3.7 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/curation_notes.txt\nCompleted 602.7 KiB/707.4 KiB (3.7 MiB/s) with 6 file(s) remaining\rCompleted 631.5 KiB/707.4 KiB (3.8 MiB/s) with 6 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/curation_image.jpeg\nCompleted 631.5 KiB/707.4 KiB (3.8 MiB/s) with 5 file(s) remaining\rCompleted 633.2 KiB/707.4 KiB (3.4 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/manifest.xml\nCompleted 633.2 KiB/707.4 KiB (3.4 MiB/s) with 4 file(s) remaining\rCompleted 649.1 KiB/707.4 KiB (3.3 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000703-octave.m to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/BIOMD0000000703-octave.m\nCompleted 649.1 KiB/707.4 KiB (3.3 MiB/s) with 3 file(s) remaining\rCompleted 661.3 KiB/707.4 KiB (3.2 MiB/s) with 3 file(s) remaining\rCompleted 677.2 KiB/707.4 KiB (3.3 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000703-matlab.m to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/BIOMD0000000703-matlab.m\nCompleted 677.2 KiB/707.4 KiB (3.3 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000703.ode to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/BIOMD0000000703.ode\nCompleted 677.2 KiB/707.4 KiB (3.3 MiB/s) with 1 file(s) remaining\rCompleted 707.4 KiB/707.4 KiB (2.9 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000703-biopax3.owl to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/contents/BIOMD0000000703-biopax3.owl\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (134.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f167ee26f4323c9002c6/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Diedrichs2018.sedml\ncreating dataset /Diedrichs2018.sedml/autogen_report_for_task1, shape: (76, 1001), type: float64\ndataset created, uuid: d-63453ed2-1e6e867c-a034-80488b-355f75, chunk_size: (76, 1001)\ncreating dataset /Diedrichs2018.sedml/plot_1_task1, shape: (15, 1001), type: float64\ndataset created, uuid: d-63453ed2-1e6e867c-7879-f7b811-111968, chunk_size: (15, 1001)\ncreating attribute combineArchiveLocation in /Diedrichs2018.sedml\ncreating attribute uri in /Diedrichs2018.sedml\ncreating attribute _type in /Diedrichs2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Diedrichs2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Diedrichs2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Diedrichs2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Diedrichs2018.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Diedrichs2018.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Diedrichs2018.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Diedrichs2018.sedml/autogen_report_for_task1\ncreating attribute uri in /Diedrichs2018.sedml/autogen_report_for_task1\ncreating attribute _type in /Diedrichs2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Diedrichs2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Diedrichs2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Diedrichs2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Diedrichs2018.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Diedrichs2018.sedml/plot_1_task1\ncreating attribute sedmlId in /Diedrichs2018.sedml/plot_1_task1\ncreating attribute sedmlName in /Diedrichs2018.sedml/plot_1_task1\ncreating attribute uri in /Diedrichs2018.sedml/plot_1_task1\ncreate_links: /\ngot link: Diedrichs2018.sedml\ncreate_links: /Diedrichs2018.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Diedrichs2018.sedml/autogen_report_for_task1 to tgt: /Diedrichs2018.sedml/autogen_report_for_task1, shape: (76, 1001), type: float64\niterating over chunks for /Diedrichs2018.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 76, 1), slice(0, 1001, 1))\ndone with dataload for /Diedrichs2018.sedml/autogen_report_for_task1\nwrite_dataset src: /Diedrichs2018.sedml/plot_1_task1 to tgt: /Diedrichs2018.sedml/plot_1_task1, shape: (15, 1001), type: float64\niterating over chunks for /Diedrichs2018.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 15, 1), slice(0, 1001, 1))\ndone with dataload for /Diedrichs2018.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f167ee26f4323c9002c6\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.\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.943502,"sedDocuments":[{"location":"Diedrichs2018.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  Diedrichs2018.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 76 data sets\r\n    Plots (1):\r\n      plot_1_task1: 14 curves\r\n\r\nExecuting SED-ML file 1: Diedrichs2018.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":1.461355,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.320751,"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":0.490409,"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":"p1_curve_11_task1","status":"SUCCEEDED"},{"id":"p1_curve_12_task1","status":"SUCCEEDED"},{"id":"p1_curve_13_task1","status":"SUCCEEDED"},{"id":"p1_curve_14_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.454352,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_Ip","status":"SUCCEEDED"},{"id":"autogen_task1_Pp","status":"SUCCEEDED"},{"id":"autogen_task1_A4","status":"SUCCEEDED"},{"id":"autogen_task1_A6","status":"SUCCEEDED"},{"id":"autogen_task1_Btot","status":"SUCCEEDED"},{"id":"autogen_task1_C","status":"SUCCEEDED"},{"id":"autogen_task1_Ep","status":"SUCCEEDED"},{"id":"autogen_task1_G","status":"SUCCEEDED"},{"id":"autogen_task1_U","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_g","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_KBU","status":"SUCCEEDED"},{"id":"autogen_task1_KBP","status":"SUCCEEDED"},{"id":"autogen_task1_KBA6","status":"SUCCEEDED"},{"id":"autogen_task1_A6tot_norm","status":"SUCCEEDED"},{"id":"autogen_task1_CHOP_BiP_ratio","status":"SUCCEEDED"},{"id":"autogen_task1_G_star","status":"SUCCEEDED"},{"id":"autogen_task1_C_star","status":"SUCCEEDED"},{"id":"autogen_task1_A4_star","status":"SUCCEEDED"},{"id":"autogen_task1_U_star","status":"SUCCEEDED"},{"id":"autogen_task1_A6_star","status":"SUCCEEDED"},{"id":"autogen_task1_b_star","status":"SUCCEEDED"},{"id":"autogen_task1_c_star","status":"SUCCEEDED"},{"id":"autogen_task1_g_star","status":"SUCCEEDED"},{"id":"autogen_task1_Btot_star","status":"SUCCEEDED"},{"id":"autogen_task1_kdB","status":"SUCCEEDED"},{"id":"autogen_task1_kdb","status":"SUCCEEDED"},{"id":"autogen_task1_kdA4","status":"SUCCEEDED"},{"id":"autogen_task1_kdA6","status":"SUCCEEDED"},{"id":"autogen_task1_kdc","status":"SUCCEEDED"},{"id":"autogen_task1_kdC","status":"SUCCEEDED"},{"id":"autogen_task1_kdg","status":"SUCCEEDED"},{"id":"autogen_task1_kdG","status":"SUCCEEDED"},{"id":"autogen_task1_Ep_star","status":"SUCCEEDED"},{"id":"autogen_task1_Stress","status":"SUCCEEDED"},{"id":"autogen_task1_Etot_norm","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_x_star","status":"SUCCEEDED"},{"id":"autogen_task1_xtot_norm","status":"SUCCEEDED"},{"id":"autogen_task1_kdx","status":"SUCCEEDED"},{"id":"autogen_task1_KUP","status":"SUCCEEDED"},{"id":"autogen_task1_KBI","status":"SUCCEEDED"},{"id":"autogen_task1_KUI","status":"SUCCEEDED"},{"id":"autogen_task1_KOperk","status":"SUCCEEDED"},{"id":"autogen_task1_KOire1","status":"SUCCEEDED"},{"id":"autogen_task1_fi","status":"SUCCEEDED"},{"id":"autogen_task1_alphaI","status":"SUCCEEDED"},{"id":"autogen_task1_Ip_star","status":"SUCCEEDED"},{"id":"autogen_task1_betaI","status":"SUCCEEDED"},{"id":"autogen_task1_ER","status":"SUCCEEDED"},{"id":"autogen_task1_Btot_degr","status":"SUCCEEDED"},{"id":"autogen_task1_b_syn","status":"SUCCEEDED"},{"id":"autogen_task1_b_degr","status":"SUCCEEDED"},{"id":"autogen_task1_A6_degr","status":"SUCCEEDED"},{"id":"autogen_task1_A6_syn","status":"SUCCEEDED"},{"id":"autogen_task1_U_degr","status":"SUCCEEDED"},{"id":"autogen_task1_A4_syn","status":"SUCCEEDED"},{"id":"autogen_task1_A4_degr","status":"SUCCEEDED"},{"id":"autogen_task1_c_syn","status":"SUCCEEDED"},{"id":"autogen_task1_c_degr","status":"SUCCEEDED"},{"id":"autogen_task1_C_syn","status":"SUCCEEDED"},{"id":"autogen_task1_C_degr","status":"SUCCEEDED"},{"id":"autogen_task1_g_syn","status":"SUCCEEDED"},{"id":"autogen_task1_g_degr","status":"SUCCEEDED"},{"id":"autogen_task1_G_syn","status":"SUCCEEDED"},{"id":"autogen_task1_G_degr","status":"SUCCEEDED"},{"id":"autogen_task1_Ep_degr","status":"SUCCEEDED"},{"id":"autogen_task1_U_syn","status":"SUCCEEDED"},{"id":"autogen_task1_Btot_syn","status":"SUCCEEDED"},{"id":"autogen_task1_Ep_syn","status":"SUCCEEDED"},{"id":"autogen_task1_x_degr","status":"SUCCEEDED"},{"id":"autogen_task1_x_syn","status":"SUCCEEDED"}]}]}]}