{"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    438      0 --:--:-- --:--:-- --:--:--   437\n\r100  137k  100  137k    0     0   325k      0 --:--:-- --:--:-- --:--:--  325k\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 (28.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/rawLog.txt\nCompleted 3.1 KiB/3.1 KiB (48.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000130_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000130_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/reports.h5 (deflated 74%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 32.2 KiB/32.2 KiB (420.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/outputs/reports.h5\nCompleted 10.8 KiB/38.9 KiB (117.2 KiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000130_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/outputs/BIOMD0000000130_url.sedml/autogen_plot_for_task1.pdf\nCompleted 10.8 KiB/38.9 KiB (117.2 KiB/s) with 3 file(s) remaining\rCompleted 18.0 KiB/38.9 KiB (178.9 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/outputs/plots.zip\nCompleted 18.0 KiB/38.9 KiB (178.9 KiB/s) with 2 file(s) remaining\rCompleted 36.2 KiB/38.9 KiB (319.1 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/output.zip\nCompleted 36.2 KiB/38.9 KiB (319.1 KiB/s) with 1 file(s) remaining\rCompleted 38.9 KiB/38.9 KiB (308.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000130-biopax2.owl  \n  inflating: contents/BIOMD0000000130-biopax3.owl  \n  inflating: contents/BIOMD0000000130-matlab.m  \n  inflating: contents/BIOMD0000000130-octave.m  \n  inflating: contents/BIOMD0000000130.m  \n  inflating: contents/BIOMD0000000130.pdf  \n  inflating: contents/BIOMD0000000130.png  \n  inflating: contents/BIOMD0000000130.svg  \n  inflating: contents/BIOMD0000000130_url.sedml  \n  inflating: contents/BIOMD0000000130_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 3.6 KiB/201.3 KiB (54.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000130-biopax2.owl to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/BIOMD0000000130-biopax2.owl\nCompleted 3.6 KiB/201.3 KiB (54.9 KiB/s) with 13 file(s) remaining\rCompleted 8.7 KiB/201.3 KiB (76.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000130.png to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/BIOMD0000000130.png\nCompleted 8.7 KiB/201.3 KiB (76.5 KiB/s) with 12 file(s) remaining\rCompleted 9.5 KiB/201.3 KiB (76.2 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000130.svg to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/BIOMD0000000130.svg\nCompleted 9.5 KiB/201.3 KiB (76.2 KiB/s) with 11 file(s) remaining\rCompleted 144.2 KiB/201.3 KiB (1.1 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000130.pdf to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/BIOMD0000000130.pdf\nCompleted 144.2 KiB/201.3 KiB (1.1 MiB/s) with 10 file(s) remaining\rCompleted 159.9 KiB/201.3 KiB (1.1 MiB/s) with 10 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/curation_image.png\nCompleted 159.9 KiB/201.3 KiB (1.1 MiB/s) with 9 file(s) remaining\rCompleted 166.9 KiB/201.3 KiB (1.2 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000130_url.sedml to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/BIOMD0000000130_url.sedml\nCompleted 166.9 KiB/201.3 KiB (1.2 MiB/s) with 8 file(s) remaining\rCompleted 170.6 KiB/201.3 KiB (1.2 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000130-biopax3.owl to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/BIOMD0000000130-biopax3.owl\nCompleted 170.6 KiB/201.3 KiB (1.2 MiB/s) with 7 file(s) remaining\rCompleted 174.3 KiB/201.3 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000130.m to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/BIOMD0000000130.m\nCompleted 174.3 KiB/201.3 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 177.9 KiB/201.3 KiB (1.2 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000130-matlab.m to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/BIOMD0000000130-matlab.m\nCompleted 177.9 KiB/201.3 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 181.5 KiB/201.3 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000130-octave.m to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/BIOMD0000000130-octave.m\nCompleted 181.5 KiB/201.3 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 181.5 KiB/201.3 KiB (1.0 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/curation_notes.txt\nCompleted 181.5 KiB/201.3 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 196.1 KiB/201.3 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000130_url.xml to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/BIOMD0000000130_url.xml\nCompleted 196.1 KiB/201.3 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 199.7 KiB/201.3 KiB (1.0 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/metadata.rdf\nCompleted 199.7 KiB/201.3 KiB (1.0 MiB/s) with 1 file(s) remaining\rCompleted 201.3 KiB/201.3 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.2 KiB/8.2 KiB (128.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c426321246e8866d9ff6/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000130_url.sedml\ncreating dataset /BIOMD0000000130_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-13fdb109-1d9d5b64-9d39-8b461a-d7ea6b, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000130_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-13fdb109-1d9d5b64-6197-413046-c8bae8, chunk_size: (10, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000130_url.sedml\ncreating attribute uri in /BIOMD0000000130_url.sedml\ncreating attribute _type in /BIOMD0000000130_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000130_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000130_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000130_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000130_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000130_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000130_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000130_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000130_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000130_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000130_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000130_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000130_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000130_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000130_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000130_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000130_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000130_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000130_url.sedml\ncreate_links: /BIOMD0000000130_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000130_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000130_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000130_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000130_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000130_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000130_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000130_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000130_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c426321246e8866d9ff6\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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.376487,"sedDocuments":[{"location":"BIOMD0000000130_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  BIOMD0000000130_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 10 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 8 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000130_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":0.965146,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.177109,"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":0.149884,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_a","status":"SUCCEEDED"},{"id":"autogen_task1_b","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_Vthresh","status":"SUCCEEDED"},{"id":"autogen_task1_i","status":"SUCCEEDED"},{"id":"autogen_task1_v","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.51656,"curves":[{"id":"autogen_curve_task1_a","status":"SUCCEEDED"},{"id":"autogen_curve_task1_b","status":"SUCCEEDED"},{"id":"autogen_curve_task1_c","status":"SUCCEEDED"},{"id":"autogen_curve_task1_d","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Vthresh","status":"SUCCEEDED"},{"id":"autogen_curve_task1_i","status":"SUCCEEDED"},{"id":"autogen_curve_task1_v","status":"SUCCEEDED"},{"id":"autogen_curve_task1_u","status":"SUCCEEDED"}]}]}]}