{"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    417      0 --:--:-- --:--:-- --:--:--   418\n\r100  160k  100  160k    0     0   362k      0 --:--:-- --:--:-- --:--:--  362k\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/64710ac39a62a8be53f7a7d6/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (52.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/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/BIOMD0000000291_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000291_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 16%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 130.7 KiB/130.7 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/outputs/reports.h5\nCompleted 119.0 KiB/139.1 KiB (1.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/output.zip\nCompleted 119.0 KiB/139.1 KiB (1.4 MiB/s) with 3 file(s) remaining\rCompleted 126.1 KiB/139.1 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/outputs/plots.zip\nCompleted 126.1 KiB/139.1 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 136.5 KiB/139.1 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000291_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/outputs/BIOMD0000000291_url.sedml/autogen_plot_for_task1.pdf\nCompleted 136.5 KiB/139.1 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 139.1 KiB/139.1 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000291-biopax2.owl  \n  inflating: contents/BIOMD0000000291-biopax3.owl  \n  inflating: contents/BIOMD0000000291-matlab.m  \n  inflating: contents/BIOMD0000000291-octave.m  \n  inflating: contents/BIOMD0000000291.m  \n  inflating: contents/BIOMD0000000291.ode  \n  inflating: contents/BIOMD0000000291.pdf  \n  inflating: contents/BIOMD0000000291.png  \n  inflating: contents/BIOMD0000000291.sci  \n  inflating: contents/BIOMD0000000291.svg  \n  inflating: contents/BIOMD0000000291_url.sedml  \n  inflating: contents/BIOMD0000000291_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 7.1 KiB/~250.0 KiB (100.5 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000291-biopax2.owl to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291-biopax2.owl\nCompleted 7.1 KiB/~250.0 KiB (100.5 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 11.8 KiB/255.0 KiB (105.3 KiB/s) with 15 file(s) remaining                  \rupload: contents/BIOMD0000000291-matlab.m to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291-matlab.m\nCompleted 11.8 KiB/255.0 KiB (105.3 KiB/s) with 14 file(s) remaining\rCompleted 16.9 KiB/255.0 KiB (137.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000291.png to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291.png\nCompleted 16.9 KiB/255.0 KiB (137.5 KiB/s) with 13 file(s) remaining\rCompleted 21.6 KiB/255.0 KiB (173.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000291-octave.m to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291-octave.m\nCompleted 21.6 KiB/255.0 KiB (173.8 KiB/s) with 12 file(s) remaining\rCompleted 24.0 KiB/255.0 KiB (170.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000291.sci to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291.sci\nCompleted 24.0 KiB/255.0 KiB (170.8 KiB/s) with 11 file(s) remaining\rCompleted 26.4 KiB/255.0 KiB (186.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000291.ode to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291.ode\nCompleted 26.4 KiB/255.0 KiB (186.4 KiB/s) with 10 file(s) remaining\rCompleted 40.9 KiB/255.0 KiB (273.3 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000291_url.sedml to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291_url.sedml\nCompleted 40.9 KiB/255.0 KiB (273.3 KiB/s) with 9 file(s) remaining\rCompleted 44.0 KiB/255.0 KiB (273.0 KiB/s) with 9 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/metadata.rdf\nCompleted 44.0 KiB/255.0 KiB (273.0 KiB/s) with 8 file(s) remaining\rCompleted 76.2 KiB/255.0 KiB (469.0 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/curation_image.png\nCompleted 76.2 KiB/255.0 KiB (469.0 KiB/s) with 7 file(s) remaining\rCompleted 94.4 KiB/255.0 KiB (521.3 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000291_url.xml to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291_url.xml\nCompleted 94.4 KiB/255.0 KiB (521.3 KiB/s) with 6 file(s) remaining\rCompleted 99.1 KiB/255.0 KiB (495.5 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000291.m to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291.m\nCompleted 99.1 KiB/255.0 KiB (495.5 KiB/s) with 5 file(s) remaining\rCompleted 100.0 KiB/255.0 KiB (488.8 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000291.svg to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291.svg\nCompleted 100.0 KiB/255.0 KiB (488.8 KiB/s) with 4 file(s) remaining\rCompleted 244.6 KiB/255.0 KiB (1.2 MiB/s) with 4 file(s) remaining  \rupload: contents/BIOMD0000000291.pdf to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291.pdf\nCompleted 244.6 KiB/255.0 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 252.7 KiB/255.0 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000291-biopax3.owl to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/BIOMD0000000291-biopax3.owl\nCompleted 252.7 KiB/255.0 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 254.6 KiB/255.0 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/manifest.xml\nCompleted 254.6 KiB/255.0 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 255.0 KiB/255.0 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/contents/curation_notes.txt\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.8 KiB/8.8 KiB (138.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ac39a62a8be53f7a7d6/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000291_url.sedml\ncreating dataset /BIOMD0000000291_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\ndataset created, uuid: d-c12e81b1-558b015b-c6f5-3b0c52-78eaab, chunk_size: (11, 1001)\ncreating dataset /BIOMD0000000291_url.sedml/autogen_report_for_task1, shape: (25, 1001), type: float64\ndataset created, uuid: d-c12e81b1-558b015b-3660-5ce456-d0141a, chunk_size: (25, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000291_url.sedml\ncreating attribute uri in /BIOMD0000000291_url.sedml\ncreating attribute _type in /BIOMD0000000291_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000291_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000291_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000291_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000291_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000291_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000291_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000291_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000291_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000291_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000291_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000291_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000291_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000291_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000291_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000291_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000291_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000291_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000291_url.sedml\ncreate_links: /BIOMD0000000291_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000291_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000291_url.sedml/autogen_plot_for_task1, shape: (11, 1001), type: float64\niterating over chunks for /BIOMD0000000291_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 11, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000291_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000291_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000291_url.sedml/autogen_report_for_task1, shape: (25, 1001), type: float64\niterating over chunks for /BIOMD0000000291_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 25, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000291_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710ac39a62a8be53f7a7d6\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 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.\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":1.667289,"sedDocuments":[{"location":"BIOMD0000000291_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  BIOMD0000000291_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 25 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 10 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000291_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":1.161792,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.238784,"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":0.221065,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_x1","status":"SUCCEEDED"},{"id":"autogen_task1_x2","status":"SUCCEEDED"},{"id":"autogen_task1_x3","status":"SUCCEEDED"},{"id":"autogen_task1_x4","status":"SUCCEEDED"},{"id":"autogen_task1_x5","status":"SUCCEEDED"},{"id":"autogen_task1_x6","status":"SUCCEEDED"},{"id":"autogen_task1_x7","status":"SUCCEEDED"},{"id":"autogen_task1_A0","status":"SUCCEEDED"},{"id":"autogen_task1_B0","status":"SUCCEEDED"},{"id":"autogen_task1_C0","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_k5","status":"SUCCEEDED"},{"id":"autogen_task1_k6","status":"SUCCEEDED"},{"id":"autogen_task1_k7","status":"SUCCEEDED"},{"id":"autogen_task1_k8","status":"SUCCEEDED"},{"id":"autogen_task1_k9","status":"SUCCEEDED"},{"id":"autogen_task1_k10","status":"SUCCEEDED"},{"id":"autogen_task1_K_AlB","status":"SUCCEEDED"},{"id":"autogen_task1_K_AlB2","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.575343,"curves":[{"id":"autogen_curve_task1_x1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x5","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x6","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x7","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A0","status":"SUCCEEDED"},{"id":"autogen_curve_task1_B0","status":"SUCCEEDED"},{"id":"autogen_curve_task1_C0","status":"SUCCEEDED"}]}]}]}