{"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    448      0 --:--:-- --:--:-- --:--:--   448\n\r100  266k  100  266k    0     0   618k      0 --:--:-- --:--:-- --:--:--  618k\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 (23.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/rawLog.txt\nCompleted 2.4 KiB/2.4 KiB (34.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 73%)\n  adding: outputs/BIOMD0000000629_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000629_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 23%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 106.1 KiB/106.1 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/outputs/reports.h5\nCompleted 90.5 KiB/108.0 KiB (1015.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/output.zip\nCompleted 90.5 KiB/108.0 KiB (1015.3 KiB/s) with 3 file(s) remaining\rCompleted 96.4 KiB/108.0 KiB (856.9 KiB/s) with 3 file(s) remaining \rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/outputs/plots.zip\nCompleted 96.4 KiB/108.0 KiB (856.9 KiB/s) with 2 file(s) remaining\rCompleted 105.3 KiB/108.0 KiB (803.8 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000629_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/outputs/BIOMD0000000629_url.sedml/autogen_plot_for_task1.pdf\nCompleted 105.3 KiB/108.0 KiB (803.8 KiB/s) with 1 file(s) remaining\rCompleted 108.0 KiB/108.0 KiB (782.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000629-biopax2.owl  \n  inflating: contents/BIOMD0000000629-biopax3.owl  \n  inflating: contents/BIOMD0000000629-matlab.m  \n  inflating: contents/BIOMD0000000629-octave.m  \n  inflating: contents/BIOMD0000000629.m  \n  inflating: contents/BIOMD0000000629.ode  \n  inflating: contents/BIOMD0000000629.pdf  \n  inflating: contents/BIOMD0000000629.png  \n  inflating: contents/BIOMD0000000629.sci  \n  inflating: contents/BIOMD0000000629.svg  \n  inflating: contents/BIOMD0000000629.vcml  \n  inflating: contents/BIOMD0000000629_url.sedml  \n  inflating: contents/BIOMD0000000629_url.xml  \n  inflating: contents/SigmaplotFiles.zip  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 8.5 KiB/~393.0 KiB (135.1 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000629-biopax2.owl to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629-biopax2.owl\nCompleted 8.5 KiB/~393.0 KiB (135.1 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 12.1 KiB/426.8 KiB (101.7 KiB/s) with 17 file(s) remaining                  \rupload: contents/BIOMD0000000629-octave.m to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629-octave.m\nCompleted 12.1 KiB/426.8 KiB (101.7 KiB/s) with 16 file(s) remaining\rCompleted 15.7 KiB/426.8 KiB (129.9 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000629-matlab.m to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629-matlab.m\nCompleted 15.7 KiB/426.8 KiB (129.9 KiB/s) with 15 file(s) remaining\rCompleted 32.0 KiB/426.8 KiB (261.2 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000629.png to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629.png\nCompleted 32.0 KiB/426.8 KiB (261.2 KiB/s) with 14 file(s) remaining\rCompleted 33.8 KiB/426.8 KiB (254.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000629.sci to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629.sci\nCompleted 33.8 KiB/426.8 KiB (254.0 KiB/s) with 13 file(s) remaining\rCompleted 39.7 KiB/426.8 KiB (272.3 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000629.svg to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629.svg\nCompleted 39.7 KiB/426.8 KiB (272.3 KiB/s) with 12 file(s) remaining\rCompleted 71.2 KiB/426.8 KiB (468.7 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000629_url.xml to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629_url.xml\nCompleted 71.2 KiB/426.8 KiB (468.7 KiB/s) with 11 file(s) remaining\rCompleted 128.9 KiB/426.8 KiB (803.9 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000629.vcml to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629.vcml\nCompleted 128.9 KiB/426.8 KiB (803.9 KiB/s) with 10 file(s) remaining\rCompleted 135.2 KiB/426.8 KiB (813.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000629_url.sedml to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629_url.sedml\nCompleted 135.2 KiB/426.8 KiB (813.7 KiB/s) with 9 file(s) remaining\rCompleted 135.6 KiB/426.8 KiB (744.8 KiB/s) with 9 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/curation_notes.txt\nCompleted 135.6 KiB/426.8 KiB (744.8 KiB/s) with 8 file(s) remaining\rCompleted 137.7 KiB/426.8 KiB (747.5 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/manifest.xml\nCompleted 137.7 KiB/426.8 KiB (747.5 KiB/s) with 7 file(s) remaining\rCompleted 222.6 KiB/426.8 KiB (1.2 MiB/s) with 7 file(s) remaining  \rupload: contents/SigmaplotFiles.zip to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/SigmaplotFiles.zip\nCompleted 222.6 KiB/426.8 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 228.4 KiB/426.8 KiB (1.2 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/metadata.rdf\nCompleted 228.4 KiB/426.8 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 253.9 KiB/426.8 KiB (1.3 MiB/s) with 5 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/curation_image.png\nCompleted 253.9 KiB/426.8 KiB (1.3 MiB/s) with 4 file(s) remaining\rCompleted 265.4 KiB/426.8 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000629-biopax3.owl to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629-biopax3.owl\nCompleted 265.4 KiB/426.8 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 268.9 KiB/426.8 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000629.m to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629.m\nCompleted 268.9 KiB/426.8 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 425.1 KiB/426.8 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000629.pdf to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629.pdf\nCompleted 425.1 KiB/426.8 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 426.8 KiB/426.8 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000629.ode to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/contents/BIOMD0000000629.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.5 KiB/9.5 KiB (84.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b6e49c0d898ffdf0e1e/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000629_url.sedml\ncreating dataset /BIOMD0000000629_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-3aeaab34-74fdbad6-59c9-a4799f-162504, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000629_url.sedml/autogen_report_for_task1, shape: (9, 1001), type: float64\ndataset created, uuid: d-3aeaab34-74fdbad6-a369-d79cfa-2610e5, chunk_size: (9, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000629_url.sedml\ncreating attribute uri in /BIOMD0000000629_url.sedml\ncreating attribute _type in /BIOMD0000000629_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000629_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000629_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000629_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000629_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000629_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000629_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000629_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000629_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000629_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000629_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000629_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000629_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000629_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000629_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000629_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000629_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000629_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000629_url.sedml\ncreate_links: /BIOMD0000000629_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000629_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000629_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000629_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000629_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000629_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000629_url.sedml/autogen_report_for_task1, shape: (9, 1001), type: float64\niterating over chunks for /BIOMD0000000629_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000629_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711b6e49c0d898ffdf0e1e\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.\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.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file 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":17.337524,"sedDocuments":[{"location":"BIOMD0000000629_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  BIOMD0000000629_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 9 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000629_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":17.031703,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":16.503877,"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":0.122697,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_L","status":"SUCCEEDED"},{"id":"autogen_task1_LR","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_CA","status":"SUCCEEDED"},{"id":"autogen_task1_LRCA","status":"SUCCEEDED"},{"id":"autogen_task1_RAR_retinoids","status":"SUCCEEDED"},{"id":"autogen_task1_LR_complx","status":"SUCCEEDED"},{"id":"autogen_task1_LRCA_complx","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.290112,"curves":[{"id":"autogen_curve_task1_L","status":"SUCCEEDED"},{"id":"autogen_curve_task1_LR","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_LRCA","status":"SUCCEEDED"}]}]}]}