{"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    288      0 --:--:-- --:--:-- --:--:--   287\r100   139  100   139    0     0    287      0 --:--:-- --:--:-- --:--:--   287\n\r100  191k  100  191k    0     0   321k      0 --:--:-- --:--:-- --:--:--  321k\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 (28.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/rawLog.txt\nCompleted 3.2 KiB/3.2 KiB (42.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/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/BIOMD0000000258_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000258_url.sedml/autogen_plot_for_task1.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 21%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 101.8 KiB/101.8 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/outputs/reports.h5\nCompleted 91.0 KiB/113.0 KiB (1013.8 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/output.zip\nCompleted 91.0 KiB/113.0 KiB (1013.8 KiB/s) with 3 file(s) remaining\rCompleted 98.9 KiB/113.0 KiB (967.9 KiB/s) with 3 file(s) remaining \rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/outputs/plots.zip\nCompleted 98.9 KiB/113.0 KiB (967.9 KiB/s) with 2 file(s) remaining\rCompleted 110.3 KiB/113.0 KiB (954.0 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000258_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/outputs/BIOMD0000000258_url.sedml/autogen_plot_for_task1.pdf\nCompleted 110.3 KiB/113.0 KiB (954.0 KiB/s) with 1 file(s) remaining\rCompleted 113.0 KiB/113.0 KiB (952.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000258-biopax2.owl  \n  inflating: contents/BIOMD0000000258-biopax3.owl  \n  inflating: contents/BIOMD0000000258-matlab.m  \n  inflating: contents/BIOMD0000000258-octave.m  \n  inflating: contents/BIOMD0000000258.m  \n  inflating: contents/BIOMD0000000258.ode  \n  inflating: contents/BIOMD0000000258.pdf  \n  inflating: contents/BIOMD0000000258.png  \n  inflating: contents/BIOMD0000000258.sci  \n  inflating: contents/BIOMD0000000258.svg  \n  inflating: contents/BIOMD0000000258.vcml  \n  inflating: contents/BIOMD0000000258_url.sedml  \n  inflating: contents/BIOMD0000000258_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 8.1 KiB/~298.1 KiB (118.1 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000258-biopax2.owl to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258-biopax2.owl\nCompleted 8.1 KiB/~298.1 KiB (118.1 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 9.8 KiB/304.9 KiB (79.8 KiB/s) with 16 file(s) remaining                    \rupload: contents/BIOMD0000000258.sci to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258.sci\nCompleted 9.8 KiB/304.9 KiB (79.8 KiB/s) with 15 file(s) remaining\rCompleted 13.5 KiB/304.9 KiB (106.8 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000258.m to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258.m\nCompleted 13.5 KiB/304.9 KiB (106.8 KiB/s) with 14 file(s) remaining\rCompleted 31.6 KiB/304.9 KiB (246.7 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000258.png to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258.png\nCompleted 31.6 KiB/304.9 KiB (246.7 KiB/s) with 13 file(s) remaining\rCompleted 42.9 KiB/304.9 KiB (318.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000258-biopax3.owl to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258-biopax3.owl\nCompleted 42.9 KiB/304.9 KiB (318.9 KiB/s) with 12 file(s) remaining\rCompleted 56.4 KiB/304.9 KiB (409.0 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000258_url.xml to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258_url.xml\nCompleted 56.4 KiB/304.9 KiB (409.0 KiB/s) with 11 file(s) remaining\rCompleted 64.8 KiB/304.9 KiB (423.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000258.svg to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258.svg\nCompleted 64.8 KiB/304.9 KiB (423.8 KiB/s) with 10 file(s) remaining\rCompleted 84.7 KiB/304.9 KiB (540.6 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000258.vcml to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258.vcml\nCompleted 84.7 KiB/304.9 KiB (540.6 KiB/s) with 9 file(s) remaining\rCompleted 94.8 KiB/304.9 KiB (575.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000258_url.sedml to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258_url.sedml\nCompleted 94.8 KiB/304.9 KiB (575.0 KiB/s) with 8 file(s) remaining\rCompleted 96.7 KiB/304.9 KiB (551.7 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000258.ode to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258.ode\nCompleted 96.7 KiB/304.9 KiB (551.7 KiB/s) with 7 file(s) remaining\rCompleted 100.4 KiB/304.9 KiB (540.1 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000258-octave.m to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258-octave.m\nCompleted 100.4 KiB/304.9 KiB (540.1 KiB/s) with 6 file(s) remaining\rCompleted 102.4 KiB/304.9 KiB (540.5 KiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/manifest.xml\nCompleted 102.4 KiB/304.9 KiB (540.5 KiB/s) with 5 file(s) remaining\rCompleted 107.0 KiB/304.9 KiB (556.4 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/metadata.rdf\nCompleted 107.0 KiB/304.9 KiB (556.4 KiB/s) with 4 file(s) remaining\rCompleted 110.7 KiB/304.9 KiB (568.9 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000258-matlab.m to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258-matlab.m\nCompleted 110.7 KiB/304.9 KiB (568.9 KiB/s) with 3 file(s) remaining\rCompleted 110.8 KiB/304.9 KiB (556.9 KiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/curation_notes.txt\nCompleted 110.8 KiB/304.9 KiB (556.9 KiB/s) with 2 file(s) remaining\rCompleted 259.6 KiB/304.9 KiB (1.2 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000258.pdf to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/BIOMD0000000258.pdf\nCompleted 259.6 KiB/304.9 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 304.9 KiB/304.9 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.3 KiB/9.3 KiB (96.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a559a62a8be53f79abb/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000258_url.sedml\ncreating dataset /BIOMD0000000258_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\ndataset created, uuid: d-41cd8448-2aa097b6-7fdf-03a59b-4e87d3, chunk_size: (4, 1001)\ncreating dataset /BIOMD0000000258_url.sedml/autogen_report_for_task1, shape: (18, 1001), type: float64\ndataset created, uuid: d-41cd8448-2aa097b6-aa31-7cb869-1338f0, chunk_size: (18, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000258_url.sedml\ncreating attribute uri in /BIOMD0000000258_url.sedml\ncreating attribute _type in /BIOMD0000000258_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000258_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000258_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000258_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000258_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000258_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000258_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000258_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000258_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000258_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000258_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000258_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000258_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000258_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000258_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000258_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000258_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000258_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000258_url.sedml\ncreate_links: /BIOMD0000000258_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000258_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000258_url.sedml/autogen_plot_for_task1, shape: (4, 1001), type: float64\niterating over chunks for /BIOMD0000000258_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000258_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000258_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000258_url.sedml/autogen_report_for_task1, shape: (18, 1001), type: float64\niterating over chunks for /BIOMD0000000258_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 18, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000258_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710a559a62a8be53f79abb\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve 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.\nProcess 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 SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.413799,"sedDocuments":[{"location":"BIOMD0000000258_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  BIOMD0000000258_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 18 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 3 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000258_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":0.959129,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.204291,"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":0.205667,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_r31","status":"SUCCEEDED"},{"id":"autogen_task1_r24","status":"SUCCEEDED"},{"id":"autogen_task1_Chi14","status":"SUCCEEDED"},{"id":"autogen_task1_Ks1","status":"SUCCEEDED"},{"id":"autogen_task1_Ks2","status":"SUCCEEDED"},{"id":"autogen_task1_Ks3","status":"SUCCEEDED"},{"id":"autogen_task1_Ks4","status":"SUCCEEDED"},{"id":"autogen_task1_Vm1","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.429508,"curves":[{"id":"autogen_curve_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_curve_task1_beta","status":"SUCCEEDED"},{"id":"autogen_curve_task1_gamma","status":"SUCCEEDED"}]}]}]}