{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_CA1"},{"status":"SUCCEEDED","id":"data_set_CACD"},{"status":"SUCCEEDED","id":"data_set_CACS"},{"status":"SUCCEEDED","id":"data_set_CAD"},{"status":"SUCCEEDED","id":"data_set_CAP"},{"status":"SUCCEEDED","id":"data_set_CAS"},{"status":"SUCCEEDED","id":"data_set_DKCA"},{"status":"SUCCEEDED","id":"data_set_DLEAK"},{"status":"SUCCEEDED","id":"data_set_HNA"},{"status":"SUCCEEDED","id":"data_set_HSCAN"},{"status":"SUCCEEDED","id":"data_set_I1"},{"status":"SUCCEEDED","id":"data_set_I2"},{"status":"SUCCEEDED","id":"data_set_KDR"},{"status":"SUCCEEDED","id":"data_set_MCAP"},{"status":"SUCCEEDED","id":"data_set_MNAP"},{"status":"SUCCEEDED","id":"data_set_MSCAN"},{"status":"SUCCEEDED","id":"data_set_N"},{"status":"SUCCEEDED","id":"data_set_NA"},{"status":"SUCCEEDED","id":"data_set_NAP"},{"status":"SUCCEEDED","id":"data_set_SKCA"},{"status":"SUCCEEDED","id":"data_set_SLEAK"},{"status":"SUCCEEDED","id":"data_set_VD"},{"status":"SUCCEEDED","id":"data_set_VS"}],"duration":0.187763,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_2"}],"duration":0.177175,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"10000.0","key":"total"},{"value":"qualrk","key":"meth"},{"value":"0.0","key":"t0"},{"value":"10","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000672","duration":0.439761,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.920228,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  twocompart_mnmodel.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 24 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n\r\nExecuting SED-ML file 1: twocompart_mnmodel.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `plot`\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"twocompart_mnmodel.sedml"}],"duration":1.31296,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\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    474      0 --:--:-- --:--:-- --:--:--   476\n\r100  193k  100  193k    0     0   468k      0 --:--:-- --:--:-- --:--:--  468k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mCOMBINE/OMEX archive has warnings.\r\n  - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\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 contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/readme.html    \n  inflating: contents/ramp_xpp.m     \n  inflating: contents/run_twocomp.m  \n  inflating: contents/ramp.m         \n  inflating: contents/twocompart_mnmodel.ode  \n  inflating: contents/twocompart_mnmodel.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/screenshot.jpg  \n  inflating: contents/manifest.xml   \nCompleted 1.1 KiB/295.0 KiB (9.4 KiB/s) with 9 file(s) remaining\rupload: contents/ramp.m to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/contents/ramp.m\nCompleted 1.1 KiB/295.0 KiB (9.4 KiB/s) with 8 file(s) remaining\rCompleted 2.3 KiB/295.0 KiB (18.6 KiB/s) with 8 file(s) remaining\rupload: contents/ramp_xpp.m to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/contents/ramp_xpp.m\nCompleted 2.3 KiB/295.0 KiB (18.6 KiB/s) with 7 file(s) remaining\rCompleted 3.2 KiB/295.0 KiB (24.6 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/contents/manifest.xml\nCompleted 3.2 KiB/295.0 KiB (24.6 KiB/s) with 6 file(s) remaining\rCompleted 161.3 KiB/295.0 KiB (1.0 MiB/s) with 6 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/contents/metadata.rdf\nCompleted 161.3 KiB/295.0 KiB (1.0 MiB/s) with 5 file(s) remaining\rCompleted 162.6 KiB/295.0 KiB (1014.1 KiB/s) with 5 file(s) remaining\rupload: contents/readme.html to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/contents/readme.html\nCompleted 162.6 KiB/295.0 KiB (1014.1 KiB/s) with 4 file(s) remaining\rCompleted 176.7 KiB/295.0 KiB (1.0 MiB/s) with 4 file(s) remaining   \rupload: contents/twocompart_mnmodel.sedml to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/contents/twocompart_mnmodel.sedml\nCompleted 176.7 KiB/295.0 KiB (1.0 MiB/s) with 3 file(s) remaining\rCompleted 285.5 KiB/295.0 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: contents/screenshot.jpg to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/contents/screenshot.jpg\nCompleted 285.5 KiB/295.0 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 289.6 KiB/295.0 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: contents/twocompart_mnmodel.ode to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/contents/twocompart_mnmodel.ode\nCompleted 289.6 KiB/295.0 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 295.0 KiB/295.0 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/run_twocomp.m to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/contents/run_twocomp.m\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /twocompart_mnmodel.sedml\ncreating dataset /twocompart_mnmodel.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-5228d7e1-878804c2-c019-4ae972-b5b30b, chunk_size: (2, 1001)\ncreating dataset /twocompart_mnmodel.sedml/report, shape: (24, 1001), type: float64\ndataset created, uuid: d-5228d7e1-878804c2-cccb-0656f3-f1a717, chunk_size: (24, 1001)\ncreating attribute combineArchiveLocation in /twocompart_mnmodel.sedml\ncreating attribute uri in /twocompart_mnmodel.sedml\ncreating attribute _type in /twocompart_mnmodel.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /twocompart_mnmodel.sedml/plot\ncreating attribute sedmlDataSetIds in /twocompart_mnmodel.sedml/plot\ncreating attribute sedmlDataSetLabels in /twocompart_mnmodel.sedml/plot\ncreating attribute sedmlDataSetNames in /twocompart_mnmodel.sedml/plot\ncreating attribute sedmlDataSetShapes in /twocompart_mnmodel.sedml/plot\ncreating attribute sedmlId in /twocompart_mnmodel.sedml/plot\ncreating attribute uri in /twocompart_mnmodel.sedml/plot\ncreating attribute _type in /twocompart_mnmodel.sedml/report\ncreating attribute sedmlDataSetDataTypes in /twocompart_mnmodel.sedml/report\ncreating attribute sedmlDataSetIds in /twocompart_mnmodel.sedml/report\ncreating attribute sedmlDataSetLabels in /twocompart_mnmodel.sedml/report\ncreating attribute sedmlDataSetNames in /twocompart_mnmodel.sedml/report\ncreating attribute sedmlDataSetShapes in /twocompart_mnmodel.sedml/report\ncreating attribute sedmlId in /twocompart_mnmodel.sedml/report\ncreating attribute sedmlName in /twocompart_mnmodel.sedml/report\ncreating attribute uri in /twocompart_mnmodel.sedml/report\ncreate_links: /\ngot link: twocompart_mnmodel.sedml\ncreate_links: /twocompart_mnmodel.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /twocompart_mnmodel.sedml/plot to tgt: /twocompart_mnmodel.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /twocompart_mnmodel.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /twocompart_mnmodel.sedml/plot\nwrite_dataset src: /twocompart_mnmodel.sedml/report to tgt: /twocompart_mnmodel.sedml/report, shape: (24, 1001), type: float64\niterating over chunks for /twocompart_mnmodel.sedml/report\nwriting dataset data for slice: (slice(0, 24, 1), slice(0, 1001, 1))\ndone with dataload for /twocompart_mnmodel.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42ab87550e369891baa0\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 72%)\n  adding: outputs/twocompart_mnmodel.sedml/ (stored 0%)\n  adding: outputs/twocompart_mnmodel.sedml/plot.pdf (deflated 35%)\n  adding: outputs/reports.h5 (deflated 10%)\n  adding: rawLog.txt (deflated 79%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 174.9 KiB/193.7 KiB (2.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/output.zip\nCompleted 174.9 KiB/193.7 KiB (2.2 MiB/s) with 3 file(s) remaining\rCompleted 179.3 KiB/193.7 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/outputs/plots.zip\nCompleted 179.3 KiB/193.7 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 186.2 KiB/193.7 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: outputs/twocompart_mnmodel.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/outputs/twocompart_mnmodel.sedml/plot.pdf\nCompleted 186.2 KiB/193.7 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 193.7 KiB/193.7 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/rawLog.txt\nCompleted 185.3 KiB/185.3 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/outputs/reports.h5\nCompleted 3.0 KiB/3.0 KiB (52.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42ab87550e369891baa0/outputs/log.yml\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 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.\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","skipReason":null,"exception":null,"status":"SUCCEEDED"}