{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    367      0 --:--:-- --:--:-- --:--:--   367\n\r100  186k  100  186k    0     0   373k      0 --:--:-- --:--:-- --:--:--  373k\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 (27.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (39.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/Ehrenstein1997.sedml/ (stored 0%)\n  adding: outputs/Ehrenstein1997.sedml/plot_1_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 27%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 81.7 KiB/81.7 KiB (676.7 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/outputs/reports.h5\nCompleted 5.6 KiB/84.5 KiB (55.8 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/outputs/plots.zip\nCompleted 5.6 KiB/84.5 KiB (55.8 KiB/s) with 3 file(s) remaining\rCompleted 14.2 KiB/84.5 KiB (138.0 KiB/s) with 3 file(s) remaining\rupload: outputs/Ehrenstein1997.sedml/plot_1_task1.pdf to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/outputs/Ehrenstein1997.sedml/plot_1_task1.pdf\nCompleted 14.2 KiB/84.5 KiB (138.0 KiB/s) with 2 file(s) remaining\rCompleted 81.8 KiB/84.5 KiB (757.6 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/output.zip\nCompleted 81.8 KiB/84.5 KiB (757.6 KiB/s) with 1 file(s) remaining\rCompleted 84.5 KiB/84.5 KiB (708.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000553-biopax2.owl  \n  inflating: contents/BIOMD0000000553-biopax3.owl  \n  inflating: contents/BIOMD0000000553-matlab.m  \n  inflating: contents/BIOMD0000000553-octave.m  \n  inflating: contents/BIOMD0000000553.m  \n  inflating: contents/BIOMD0000000553.ode  \n  inflating: contents/BIOMD0000000553.pdf  \n  inflating: contents/BIOMD0000000553.png  \n  inflating: contents/BIOMD0000000553.svg  \n  inflating: contents/BIOMD0000000553.vcml  \n  inflating: contents/BIOMD0000000553_url.xml  \n  inflating: contents/Ehrenstein1997.cps  \n  inflating: contents/Ehrenstein1997.sedml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 7.8 KiB/352.3 KiB (84.9 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000553-biopax2.owl to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553-biopax2.owl\nCompleted 7.8 KiB/352.3 KiB (84.9 KiB/s) with 16 file(s) remaining\rCompleted 11.7 KiB/352.3 KiB (95.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000553-matlab.m to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553-matlab.m\nCompleted 11.7 KiB/352.3 KiB (95.5 KiB/s) with 15 file(s) remaining\rCompleted 24.6 KiB/352.3 KiB (196.5 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000553.svg to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553.svg\nCompleted 24.6 KiB/352.3 KiB (196.5 KiB/s) with 14 file(s) remaining\rCompleted 28.4 KiB/352.3 KiB (222.2 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000553-octave.m to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553-octave.m\nCompleted 28.4 KiB/352.3 KiB (222.2 KiB/s) with 13 file(s) remaining\rCompleted 56.5 KiB/352.3 KiB (413.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000553.vcml to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553.vcml\nCompleted 56.5 KiB/352.3 KiB (413.8 KiB/s) with 12 file(s) remaining\rCompleted 80.6 KiB/352.3 KiB (564.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000553_url.xml to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553_url.xml\nCompleted 80.6 KiB/352.3 KiB (564.1 KiB/s) with 11 file(s) remaining\rCompleted 106.6 KiB/352.3 KiB (660.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000553.png to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553.png\nCompleted 106.6 KiB/352.3 KiB (660.7 KiB/s) with 10 file(s) remaining\rCompleted 145.1 KiB/352.3 KiB (878.3 KiB/s) with 10 file(s) remaining\rupload: contents/Ehrenstein1997.cps to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/Ehrenstein1997.cps\nCompleted 145.1 KiB/352.3 KiB (878.3 KiB/s) with 9 file(s) remaining\rCompleted 145.4 KiB/352.3 KiB (835.2 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/curation_notes.txt\nCompleted 145.4 KiB/352.3 KiB (835.2 KiB/s) with 8 file(s) remaining\rCompleted 149.8 KiB/352.3 KiB (749.4 KiB/s) with 8 file(s) remaining\rCompleted 151.7 KiB/352.3 KiB (752.0 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/manifest.xml\nCompleted 151.7 KiB/352.3 KiB (752.0 KiB/s) with 7 file(s) remaining\rCompleted 162.0 KiB/352.3 KiB (782.4 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000553-biopax3.owl to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553-biopax3.owl\nCompleted 162.0 KiB/352.3 KiB (782.4 KiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/metadata.rdf\nCompleted 162.0 KiB/352.3 KiB (782.4 KiB/s) with 5 file(s) remaining\rCompleted 165.8 KiB/352.3 KiB (790.7 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000553.m to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553.m\nCompleted 165.8 KiB/352.3 KiB (790.7 KiB/s) with 4 file(s) remaining\rCompleted 174.6 KiB/352.3 KiB (857.1 KiB/s) with 4 file(s) remaining\rupload: contents/Ehrenstein1997.sedml to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/Ehrenstein1997.sedml\nCompleted 174.6 KiB/352.3 KiB (857.1 KiB/s) with 3 file(s) remaining\rCompleted 195.4 KiB/352.3 KiB (918.5 KiB/s) with 3 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/curation_image.png\nCompleted 195.4 KiB/352.3 KiB (918.5 KiB/s) with 2 file(s) remaining\rCompleted 350.1 KiB/352.3 KiB (1.6 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000553.pdf to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553.pdf\nCompleted 350.1 KiB/352.3 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 352.3 KiB/352.3 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000553.ode to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/contents/BIOMD0000000553.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (127.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471117e49c0d898ffdeee58/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Ehrenstein1997.sedml\ncreating dataset /Ehrenstein1997.sedml/autogen_report_for_task1, shape: (13, 1001), type: float64\ndataset created, uuid: d-7a7cb267-feec99be-afd5-c840bc-cc7a2f, chunk_size: (13, 1001)\ncreating dataset /Ehrenstein1997.sedml/plot_1_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-7a7cb267-feec99be-eff3-794a83-4a2a16, chunk_size: (2, 1001)\ncreating attribute combineArchiveLocation in /Ehrenstein1997.sedml\ncreating attribute uri in /Ehrenstein1997.sedml\ncreating attribute _type in /Ehrenstein1997.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /Ehrenstein1997.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /Ehrenstein1997.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /Ehrenstein1997.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /Ehrenstein1997.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /Ehrenstein1997.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /Ehrenstein1997.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /Ehrenstein1997.sedml/autogen_report_for_task1\ncreating attribute uri in /Ehrenstein1997.sedml/autogen_report_for_task1\ncreating attribute _type in /Ehrenstein1997.sedml/plot_1_task1\ncreating attribute sedmlDataSetDataTypes in /Ehrenstein1997.sedml/plot_1_task1\ncreating attribute sedmlDataSetIds in /Ehrenstein1997.sedml/plot_1_task1\ncreating attribute sedmlDataSetLabels in /Ehrenstein1997.sedml/plot_1_task1\ncreating attribute sedmlDataSetNames in /Ehrenstein1997.sedml/plot_1_task1\ncreating attribute sedmlDataSetShapes in /Ehrenstein1997.sedml/plot_1_task1\ncreating attribute sedmlId in /Ehrenstein1997.sedml/plot_1_task1\ncreating attribute sedmlName in /Ehrenstein1997.sedml/plot_1_task1\ncreating attribute uri in /Ehrenstein1997.sedml/plot_1_task1\ncreate_links: /\ngot link: Ehrenstein1997.sedml\ncreate_links: /Ehrenstein1997.sedml\ngot link: autogen_report_for_task1\ngot link: plot_1_task1\nwrite_dataset src: /Ehrenstein1997.sedml/autogen_report_for_task1 to tgt: /Ehrenstein1997.sedml/autogen_report_for_task1, shape: (13, 1001), type: float64\niterating over chunks for /Ehrenstein1997.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 13, 1), slice(0, 1001, 1))\ndone with dataload for /Ehrenstein1997.sedml/autogen_report_for_task1\nwrite_dataset src: /Ehrenstein1997.sedml/plot_1_task1 to tgt: /Ehrenstein1997.sedml/plot_1_task1, shape: (2, 1001), type: float64\niterating over chunks for /Ehrenstein1997.sedml/plot_1_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /Ehrenstein1997.sedml/plot_1_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471117e49c0d898ffdeee58\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 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 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":1.211253,"sedDocuments":[{"location":"Ehrenstein1997.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  Ehrenstein1997.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 13 data sets\r\n    Plots (1):\r\n      plot_1_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: Ehrenstein1997.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":0.765875,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.185918,"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":0.333424,"curves":[{"id":"p1_curve_1_task1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.129259,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_aRel","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_k4","status":"SUCCEEDED"},{"id":"autogen_task1_Brain","status":"SUCCEEDED"},{"id":"autogen_task1_Loss_of_intracellular_choline","status":"SUCCEEDED"},{"id":"autogen_task1_Abeta_formation_from_APP","status":"SUCCEEDED"},{"id":"autogen_task1_Effect_of_extracellular_ACh","status":"SUCCEEDED"},{"id":"autogen_task1_Decrease_in_the_extracellular_concentration_of_beta_amyloid","status":"SUCCEEDED"}]}]}]}