{"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    451      0 --:--:-- --:--:-- --:--:--   451\n\r100  154k  100  154k    0     0   370k      0 --:--:-- --:--:-- --:--:--  370k\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 (25.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/rawLog.txt\nCompleted 2.9 KiB/2.9 KiB (49.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 74%)\n  adding: outputs/BIOMD0000000418_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000418_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 28%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 69.0 KiB/69.0 KiB (833.9 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/outputs/reports.h5\nCompleted 59.7 KiB/80.7 KiB (671.1 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/output.zip\nCompleted 59.7 KiB/80.7 KiB (671.1 KiB/s) with 3 file(s) remaining\rCompleted 70.7 KiB/80.7 KiB (647.6 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000418_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/outputs/BIOMD0000000418_url.sedml/autogen_plot_for_task1.pdf\nCompleted 70.7 KiB/80.7 KiB (647.6 KiB/s) with 2 file(s) remaining\rCompleted 78.0 KiB/80.7 KiB (681.6 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/outputs/plots.zip\nCompleted 78.0 KiB/80.7 KiB (681.6 KiB/s) with 1 file(s) remaining\rCompleted 80.7 KiB/80.7 KiB (688.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000418-biopax2.owl  \n  inflating: contents/BIOMD0000000418-biopax3.owl  \n  inflating: contents/BIOMD0000000418-matlab.m  \n  inflating: contents/BIOMD0000000418-octave.m  \n  inflating: contents/BIOMD0000000418.m  \n  inflating: contents/BIOMD0000000418.ode  \n  inflating: contents/BIOMD0000000418.pdf  \n  inflating: contents/BIOMD0000000418.png  \n  inflating: contents/BIOMD0000000418.sci  \n  inflating: contents/BIOMD0000000418.svg  \n  inflating: contents/BIOMD0000000418.vcml  \n  inflating: contents/BIOMD0000000418_url.sedml  \n  inflating: contents/BIOMD0000000418_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 4.9 KiB/240.0 KiB (68.7 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000418-biopax2.owl to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418-biopax2.owl\nCompleted 4.9 KiB/240.0 KiB (68.7 KiB/s) with 16 file(s) remaining\rCompleted 8.4 KiB/240.0 KiB (81.5 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000418-octave.m to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418-octave.m\nCompleted 8.4 KiB/240.0 KiB (81.5 KiB/s) with 15 file(s) remaining\rCompleted 11.9 KiB/240.0 KiB (104.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000418-matlab.m to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418-matlab.m\nCompleted 11.9 KiB/240.0 KiB (104.1 KiB/s) with 14 file(s) remaining\rCompleted 16.0 KiB/240.0 KiB (138.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000418.png to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418.png\nCompleted 16.0 KiB/240.0 KiB (138.6 KiB/s) with 13 file(s) remaining\rCompleted 16.2 KiB/240.0 KiB (130.5 KiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/curation_notes.txt\nCompleted 16.2 KiB/240.0 KiB (130.5 KiB/s) with 12 file(s) remaining\rCompleted 18.8 KiB/240.0 KiB (124.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000418.sci to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418.sci\nCompleted 18.8 KiB/240.0 KiB (124.7 KiB/s) with 11 file(s) remaining\rCompleted 33.6 KiB/240.0 KiB (204.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000418.vcml to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418.vcml\nCompleted 33.6 KiB/240.0 KiB (204.3 KiB/s) with 10 file(s) remaining\rCompleted 35.6 KiB/240.0 KiB (208.4 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/manifest.xml\nCompleted 35.6 KiB/240.0 KiB (208.4 KiB/s) with 9 file(s) remaining\rCompleted 44.0 KiB/240.0 KiB (254.5 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000418_url.sedml to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418_url.sedml\nCompleted 44.0 KiB/240.0 KiB (254.5 KiB/s) with 8 file(s) remaining\rCompleted 49.9 KiB/240.0 KiB (266.8 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000418-biopax3.owl to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418-biopax3.owl\nCompleted 49.9 KiB/240.0 KiB (266.8 KiB/s) with 7 file(s) remaining\rCompleted 54.1 KiB/240.0 KiB (269.4 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/metadata.rdf\nCompleted 54.1 KiB/240.0 KiB (269.4 KiB/s) with 6 file(s) remaining\rCompleted 67.0 KiB/240.0 KiB (331.3 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000418_url.xml to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418_url.xml\nCompleted 67.0 KiB/240.0 KiB (331.3 KiB/s) with 5 file(s) remaining\rCompleted 84.1 KiB/240.0 KiB (411.2 KiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/curation_image.png\nCompleted 84.1 KiB/240.0 KiB (411.2 KiB/s) with 4 file(s) remaining\rCompleted 231.5 KiB/240.0 KiB (1.0 MiB/s) with 4 file(s) remaining \rupload: contents/BIOMD0000000418.pdf to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418.pdf\nCompleted 231.5 KiB/240.0 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 235.0 KiB/240.0 KiB (1.0 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000418.m to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418.m\nCompleted 235.0 KiB/240.0 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 236.7 KiB/240.0 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000418.ode to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418.ode\nCompleted 236.7 KiB/240.0 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 240.0 KiB/240.0 KiB (954.9 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000418.svg to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/contents/BIOMD0000000418.svg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.2 KiB/9.2 KiB (146.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710c650dcacb55678bd532/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000418_url.sedml\ncreating dataset /BIOMD0000000418_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\ndataset created, uuid: d-d562ebb7-780678e1-3f75-bab93c-181ae8, chunk_size: (2, 1001)\ncreating dataset /BIOMD0000000418_url.sedml/autogen_report_for_task1, shape: (15, 1001), type: float64\ndataset created, uuid: d-d562ebb7-780678e1-7aa2-1cf025-76d4d4, chunk_size: (15, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000418_url.sedml\ncreating attribute uri in /BIOMD0000000418_url.sedml\ncreating attribute _type in /BIOMD0000000418_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000418_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000418_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000418_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000418_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000418_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000418_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000418_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000418_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000418_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000418_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000418_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000418_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000418_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000418_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000418_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000418_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000418_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000418_url.sedml\ncreate_links: /BIOMD0000000418_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000418_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000418_url.sedml/autogen_plot_for_task1, shape: (2, 1001), type: float64\niterating over chunks for /BIOMD0000000418_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000418_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000418_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000418_url.sedml/autogen_report_for_task1, shape: (15, 1001), type: float64\niterating over chunks for /BIOMD0000000418_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 15, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000418_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710c650dcacb55678bd532\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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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":1.322462,"sedDocuments":[{"location":"BIOMD0000000418_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  BIOMD0000000418_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 15 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 1 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000418_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":0.896427,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.19761,"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":0.137161,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_P","status":"SUCCEEDED"},{"id":"autogen_task1_Kd","status":"SUCCEEDED"},{"id":"autogen_task1_Ksp","status":"SUCCEEDED"},{"id":"autogen_task1_dspksp","status":"SUCCEEDED"},{"id":"autogen_task1_dspspkd","status":"SUCCEEDED"},{"id":"autogen_task1_h","status":"SUCCEEDED"},{"id":"autogen_task1_k0","status":"SUCCEEDED"},{"id":"autogen_task1_ka","status":"SUCCEEDED"},{"id":"autogen_task1_ks","status":"SUCCEEDED"},{"id":"autogen_task1_ku","status":"SUCCEEDED"},{"id":"autogen_task1_s","status":"SUCCEEDED"},{"id":"autogen_task1_univ","status":"SUCCEEDED"},{"id":"autogen_task1____r1","status":"SUCCEEDED"},{"id":"autogen_task1____r2","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.425193,"curves":[{"id":"autogen_curve_task1_P","status":"SUCCEEDED"}]}]}]}