{"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    417      0 --:--:-- --:--:-- --:--:--   416\n\r100  143k  100  143k    0     0   333k      0 --:--:-- --:--:-- --:--:--  333k\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 (26.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/rawLog.txt\nCompleted 2.6 KiB/2.6 KiB (40.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/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/reports.h5 (deflated 82%)\n  adding: outputs/BIOMD0000000141_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000141_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 29.4 KiB/29.4 KiB (428.3 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/outputs/reports.h5\nCompleted 14.8 KiB/35.3 KiB (213.5 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/output.zip\nCompleted 14.8 KiB/35.3 KiB (213.5 KiB/s) with 3 file(s) remaining\rCompleted 25.5 KiB/35.3 KiB (240.0 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000141_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/outputs/BIOMD0000000141_url.sedml/autogen_plot_for_task1.pdf\nCompleted 25.5 KiB/35.3 KiB (240.0 KiB/s) with 2 file(s) remaining\rCompleted 32.6 KiB/35.3 KiB (299.8 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/outputs/plots.zip\nCompleted 32.6 KiB/35.3 KiB (299.8 KiB/s) with 1 file(s) remaining\rCompleted 35.3 KiB/35.3 KiB (305.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000141-biopax2.owl  \n  inflating: contents/BIOMD0000000141-biopax3.owl  \n  inflating: contents/BIOMD0000000141-matlab.m  \n  inflating: contents/BIOMD0000000141-octave.m  \n  inflating: contents/BIOMD0000000141.m  \n  inflating: contents/BIOMD0000000141.ode  \n  inflating: contents/BIOMD0000000141.pdf  \n  inflating: contents/BIOMD0000000141.png  \n  inflating: contents/BIOMD0000000141.svg  \n  inflating: contents/BIOMD0000000141_url.sedml  \n  inflating: contents/BIOMD0000000141_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/199.3 KiB (51.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000141-biopax2.owl to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141-biopax2.owl\nCompleted 3.6 KiB/199.3 KiB (51.1 KiB/s) with 14 file(s) remaining\rCompleted 5.0 KiB/199.3 KiB (41.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000141.ode to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141.ode\nCompleted 5.0 KiB/199.3 KiB (41.0 KiB/s) with 13 file(s) remaining\rCompleted 12.1 KiB/199.3 KiB (94.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000141_url.sedml to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141_url.sedml\nCompleted 12.1 KiB/199.3 KiB (94.7 KiB/s) with 12 file(s) remaining\rCompleted 12.9 KiB/199.3 KiB (99.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000141.svg to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141.svg\nCompleted 12.9 KiB/199.3 KiB (99.9 KiB/s) with 11 file(s) remaining\rCompleted 16.6 KiB/199.3 KiB (124.9 KiB/s) with 11 file(s) remaining\rCompleted 19.6 KiB/199.3 KiB (146.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000141-biopax3.owl to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141-biopax3.owl\nCompleted 19.6 KiB/199.3 KiB (146.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000141-matlab.m to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141-matlab.m\nCompleted 19.6 KiB/199.3 KiB (146.7 KiB/s) with 9 file(s) remaining\rCompleted 22.7 KiB/199.3 KiB (156.0 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000141-octave.m to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141-octave.m\nCompleted 22.7 KiB/199.3 KiB (156.0 KiB/s) with 8 file(s) remaining\rCompleted 155.7 KiB/199.3 KiB (1.0 MiB/s) with 8 file(s) remaining \rupload: contents/BIOMD0000000141.pdf to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141.pdf\nCompleted 155.7 KiB/199.3 KiB (1.0 MiB/s) with 7 file(s) remaining\rCompleted 177.5 KiB/199.3 KiB (1.1 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/curation_image.png\nCompleted 177.5 KiB/199.3 KiB (1.1 MiB/s) with 6 file(s) remaining\rCompleted 179.2 KiB/199.3 KiB (1.1 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/manifest.xml\nCompleted 179.2 KiB/199.3 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 182.2 KiB/199.3 KiB (982.0 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000141.m to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141.m\nCompleted 182.2 KiB/199.3 KiB (982.0 KiB/s) with 4 file(s) remaining\rCompleted 182.3 KiB/199.3 KiB (969.0 KiB/s) with 4 file(s) remaining\rCompleted 190.6 KiB/199.3 KiB (1005.6 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000141_url.xml to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141_url.xml\nCompleted 190.6 KiB/199.3 KiB (1005.6 KiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/curation_notes.txt\nCompleted 190.6 KiB/199.3 KiB (1005.6 KiB/s) with 2 file(s) remaining\rCompleted 194.2 KiB/199.3 KiB (1004.9 KiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/metadata.rdf\nCompleted 194.2 KiB/199.3 KiB (1004.9 KiB/s) with 1 file(s) remaining\rCompleted 199.3 KiB/199.3 KiB (562.6 KiB/s) with 1 file(s) remaining \rupload: contents/BIOMD0000000141.png to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/contents/BIOMD0000000141.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.6 KiB/8.6 KiB (139.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6480c44277b666965506a92c/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000141_url.sedml\ncreating dataset /BIOMD0000000141_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-46e57fb9-2ebb65af-8b11-bf5f38-24b58b, chunk_size: (9, 1001)\ncreating dataset /BIOMD0000000141_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-46e57fb9-2ebb65af-c91d-53835f-2eecdd, chunk_size: (10, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000141_url.sedml\ncreating attribute uri in /BIOMD0000000141_url.sedml\ncreating attribute _type in /BIOMD0000000141_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000141_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000141_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000141_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000141_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000141_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000141_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000141_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000141_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000141_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000141_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000141_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000141_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000141_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000141_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000141_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000141_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000141_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000141_url.sedml\ncreate_links: /BIOMD0000000141_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000141_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000141_url.sedml/autogen_plot_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000141_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000141_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000141_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000141_url.sedml/autogen_report_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000141_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000141_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6480c44277b666965506a92c\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 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.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":15.203362,"sedDocuments":[{"location":"BIOMD0000000141_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  BIOMD0000000141_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: BIOMD0000000141_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":14.932055,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":14.273599,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.125942,"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":0.444062,"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"}]}]}]}