{"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    434      0 --:--:-- --:--:-- --:--:--   434\n\r100  290k  100  290k    0     0   664k      0 --:--:-- --:--:-- --:--:--  664k\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 (14.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (49.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 76%)\n  adding: outputs/BIOMD0000000626_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000626_url.sedml/autogen_plot_for_task1.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 164.7 KiB/164.7 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/outputs/reports.h5\nCompleted 151.9 KiB/176.7 KiB (1.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/output.zip\nCompleted 151.9 KiB/176.7 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 161.4 KiB/176.7 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/outputs/plots.zip\nCompleted 161.4 KiB/176.7 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 164.1 KiB/176.7 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/rawLog.txt\nCompleted 164.1 KiB/176.7 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 176.7 KiB/176.7 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000626_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/outputs/BIOMD0000000626_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000626-biopax2.owl  \n  inflating: contents/BIOMD0000000626-biopax3.owl  \n  inflating: contents/BIOMD0000000626-matlab.m  \n  inflating: contents/BIOMD0000000626-octave.m  \n  inflating: contents/BIOMD0000000626.m  \n  inflating: contents/BIOMD0000000626.ode  \n  inflating: contents/BIOMD0000000626.pdf  \n  inflating: contents/BIOMD0000000626.png  \n  inflating: contents/BIOMD0000000626.svg  \n  inflating: contents/BIOMD0000000626.vcml  \n  inflating: contents/BIOMD0000000626_url.sedml  \n  inflating: contents/BIOMD0000000626_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 6.4 KiB/536.9 KiB (59.7 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000626-octave.m to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626-octave.m\nCompleted 6.4 KiB/536.9 KiB (59.7 KiB/s) with 15 file(s) remaining\rCompleted 17.6 KiB/536.9 KiB (138.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000626-biopax2.owl to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626-biopax2.owl\nCompleted 17.6 KiB/536.9 KiB (138.4 KiB/s) with 14 file(s) remaining\rCompleted 34.0 KiB/536.9 KiB (243.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000626.svg to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626.svg\nCompleted 34.0 KiB/536.9 KiB (243.9 KiB/s) with 13 file(s) remaining\rCompleted 75.7 KiB/536.9 KiB (532.0 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000626.png to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626.png\nCompleted 75.7 KiB/536.9 KiB (532.0 KiB/s) with 12 file(s) remaining\rCompleted 84.6 KiB/536.9 KiB (560.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000626_url.sedml to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626_url.sedml\nCompleted 84.6 KiB/536.9 KiB (560.5 KiB/s) with 11 file(s) remaining\rCompleted 91.0 KiB/536.9 KiB (580.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000626-matlab.m to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626-matlab.m\nCompleted 91.0 KiB/536.9 KiB (580.4 KiB/s) with 10 file(s) remaining\rCompleted 157.0 KiB/536.9 KiB (990.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000626.vcml to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626.vcml\nCompleted 157.0 KiB/536.9 KiB (990.6 KiB/s) with 9 file(s) remaining\rCompleted 158.8 KiB/536.9 KiB (954.5 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/manifest.xml\nCompleted 158.8 KiB/536.9 KiB (954.5 KiB/s) with 8 file(s) remaining\rCompleted 216.5 KiB/536.9 KiB (1.2 MiB/s) with 8 file(s) remaining  \rupload: contents/BIOMD0000000626_url.xml to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626_url.xml\nCompleted 216.5 KiB/536.9 KiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 216.6 KiB/536.9 KiB (1.0 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/curation_notes.txt\nCompleted 216.6 KiB/536.9 KiB (1.0 MiB/s) with 6 file(s) remaining\rCompleted 231.1 KiB/536.9 KiB (1.0 MiB/s) with 6 file(s) remaining\rCompleted 235.4 KiB/536.9 KiB (1.0 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000626.ode to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626.ode\nCompleted 235.4 KiB/536.9 KiB (1.0 MiB/s) with 5 file(s) remaining\rCompleted 241.8 KiB/536.9 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000626.m to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626.m\nCompleted 241.8 KiB/536.9 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000626-biopax3.owl to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626-biopax3.owl\nCompleted 241.8 KiB/536.9 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 247.9 KiB/536.9 KiB (1.0 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/metadata.rdf\nCompleted 247.9 KiB/536.9 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 431.3 KiB/536.9 KiB (1.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000626.pdf to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/BIOMD0000000626.pdf\nCompleted 431.3 KiB/536.9 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 536.9 KiB/536.9 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/contents/curation_image.jpeg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (121.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b5f0dcacb55678cad26/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000626_url.sedml\ncreating dataset /BIOMD0000000626_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\ndataset created, uuid: d-236fed51-5eac0f69-1c7a-8c0167-4bda7a, chunk_size: (7, 1001)\ncreating dataset /BIOMD0000000626_url.sedml/autogen_report_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-236fed51-5eac0f69-6972-5fa511-d339b3, chunk_size: (14, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000626_url.sedml\ncreating attribute uri in /BIOMD0000000626_url.sedml\ncreating attribute _type in /BIOMD0000000626_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000626_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000626_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000626_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000626_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000626_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000626_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000626_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000626_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000626_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000626_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000626_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000626_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000626_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000626_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000626_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000626_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000626_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000626_url.sedml\ncreate_links: /BIOMD0000000626_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000626_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000626_url.sedml/autogen_plot_for_task1, shape: (7, 1001), type: float64\niterating over chunks for /BIOMD0000000626_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 7, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000626_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000626_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000626_url.sedml/autogen_report_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000626_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000626_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711b5f0dcacb55678cad26\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 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.\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":1.512346,"sedDocuments":[{"location":"BIOMD0000000626_url.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  BIOMD0000000626_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 14 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 6 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000626_url.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_plot_for_task1`\r\n      `autogen_report_for_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: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_plot_for_task1` ...","duration":0.996265,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.218592,"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":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.15192,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Rim11","status":"SUCCEEDED"},{"id":"autogen_task1_pUme6","status":"SUCCEEDED"},{"id":"autogen_task1_pSok2","status":"SUCCEEDED"},{"id":"autogen_task1_Ime1","status":"SUCCEEDED"},{"id":"autogen_task1_pIme1","status":"SUCCEEDED"},{"id":"autogen_task1_Ime2","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_rim11_1","status":"SUCCEEDED"},{"id":"autogen_task1_pume6_1","status":"SUCCEEDED"},{"id":"autogen_task1_sok2_1","status":"SUCCEEDED"},{"id":"autogen_task1_ime1_1","status":"SUCCEEDED"},{"id":"autogen_task1_pime1_1","status":"SUCCEEDED"},{"id":"autogen_task1_ime2_1","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.48994,"curves":[{"id":"autogen_curve_task1_Rim11","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pUme6","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pSok2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ime1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pIme1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ime2","status":"SUCCEEDED"}]}]}]}