{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_GNA_"},{"status":"SUCCEEDED","id":"data_set_NAI"},{"status":"SUCCEEDED","id":"data_set_V"},{"status":"SUCCEEDED","id":"data_set_VK_"},{"status":"SUCCEEDED","id":"data_set_VNA_"},{"status":"SUCCEEDED","id":"data_set_W"},{"status":"SUCCEEDED","id":"data_set_Z"}],"duration":0.097322,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.166362,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"150.0","key":"total"},{"value":"euler","key":"meth"},{"value":"0.05","key":"dt"},{"value":"0.0","key":"t0"},{"value":"3","key":"njmp"}],"algorithm":"KISAO_0000030","duration":0.085101,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.43771,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  afterdischarge-Prescott.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 8 data sets\r\n    Plots (1):\r\n      plot: 1 curves\r\n\r\nExecuting SED-ML file 1: afterdischarge-Prescott.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":"afterdischarge-Prescott.sedml"}],"duration":0.741404,"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    487      0 --:--:-- --:--:-- --:--:--   486\n\r100 15774  100 15774    0     0  40162      0 --:--:-- --:--:-- --:--:-- 40162\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/afterdischarge-Prescott.ode  \n  inflating: contents/NEURONcode/NAX.mod  \n  inflating: contents/NEURONcode/mdbetatail_s.hoc  \n  inflating: contents/NEURONcode/kdifusl.mod  \n  inflating: contents/NEURONcode/nadifusl.mod  \n  inflating: contents/NEURONcode/dbetaheadtail_jcns.hoc  \n  inflating: contents/NEURONcode/kaccum2.mod  \n  inflating: contents/NEURONcode/sbeta_jcns.hoc  \n  inflating: contents/NEURONcode/naaccum2.mod  \n  inflating: contents/NEURONcode/ht.mod  \n  inflating: contents/NEURONcode/mdbeta_s.hoc  \n  inflating: contents/afterdischarge-Prescott.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 725 Bytes/37.6 KiB (11.6 KiB/s) with 15 file(s) remaining\rupload: contents/NEURONcode/dbetaheadtail_jcns.hoc to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/NEURONcode/dbetaheadtail_jcns.hoc\nCompleted 725 Bytes/37.6 KiB (11.6 KiB/s) with 14 file(s) remaining\rCompleted 1.3 KiB/37.6 KiB (11.8 KiB/s) with 14 file(s) remaining  \rupload: contents/readme.html to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/readme.html\nCompleted 1.3 KiB/37.6 KiB (11.8 KiB/s) with 13 file(s) remaining\rCompleted 3.3 KiB/37.6 KiB (28.7 KiB/s) with 13 file(s) remaining\rupload: contents/NEURONcode/kaccum2.mod to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/NEURONcode/kaccum2.mod\nCompleted 3.3 KiB/37.6 KiB (28.7 KiB/s) with 12 file(s) remaining\rCompleted 4.7 KiB/37.6 KiB (39.9 KiB/s) with 12 file(s) remaining\rupload: contents/NEURONcode/ht.mod to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/NEURONcode/ht.mod\nCompleted 4.7 KiB/37.6 KiB (39.9 KiB/s) with 11 file(s) remaining\rCompleted 7.1 KiB/37.6 KiB (48.3 KiB/s) with 11 file(s) remaining\rupload: contents/afterdischarge-Prescott.ode to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/afterdischarge-Prescott.ode\nCompleted 7.1 KiB/37.6 KiB (48.3 KiB/s) with 10 file(s) remaining\rCompleted 12.9 KiB/37.6 KiB (81.2 KiB/s) with 10 file(s) remaining\rupload: contents/afterdischarge-Prescott.sedml to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/afterdischarge-Prescott.sedml\nCompleted 12.9 KiB/37.6 KiB (81.2 KiB/s) with 9 file(s) remaining\rCompleted 14.6 KiB/37.6 KiB (91.0 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/manifest.xml\nCompleted 14.6 KiB/37.6 KiB (91.0 KiB/s) with 8 file(s) remaining\rCompleted 21.9 KiB/37.6 KiB (133.1 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/metadata.rdf\nCompleted 21.9 KiB/37.6 KiB (133.1 KiB/s) with 7 file(s) remaining\rCompleted 26.1 KiB/37.6 KiB (146.0 KiB/s) with 7 file(s) remaining\rupload: contents/NEURONcode/NAX.mod to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/NEURONcode/NAX.mod\nCompleted 26.1 KiB/37.6 KiB (146.0 KiB/s) with 6 file(s) remaining\rCompleted 28.2 KiB/37.6 KiB (154.7 KiB/s) with 6 file(s) remaining\rupload: contents/NEURONcode/naaccum2.mod to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/NEURONcode/naaccum2.mod\nCompleted 28.2 KiB/37.6 KiB (154.7 KiB/s) with 5 file(s) remaining\rCompleted 30.8 KiB/37.6 KiB (157.6 KiB/s) with 5 file(s) remaining\rupload: contents/NEURONcode/kdifusl.mod to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/NEURONcode/kdifusl.mod\nCompleted 30.8 KiB/37.6 KiB (157.6 KiB/s) with 4 file(s) remaining\rCompleted 33.6 KiB/37.6 KiB (165.7 KiB/s) with 4 file(s) remaining\rupload: contents/NEURONcode/nadifusl.mod to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/NEURONcode/nadifusl.mod\nCompleted 33.6 KiB/37.6 KiB (165.7 KiB/s) with 3 file(s) remaining\rCompleted 35.7 KiB/37.6 KiB (174.2 KiB/s) with 3 file(s) remaining\rupload: contents/NEURONcode/sbeta_jcns.hoc to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/NEURONcode/sbeta_jcns.hoc\nCompleted 35.7 KiB/37.6 KiB (174.2 KiB/s) with 2 file(s) remaining\rCompleted 36.7 KiB/37.6 KiB (146.0 KiB/s) with 2 file(s) remaining\rupload: contents/NEURONcode/mdbeta_s.hoc to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/NEURONcode/mdbeta_s.hoc\nCompleted 36.7 KiB/37.6 KiB (146.0 KiB/s) with 1 file(s) remaining\rCompleted 37.6 KiB/37.6 KiB (132.2 KiB/s) with 1 file(s) remaining\rupload: contents/NEURONcode/mdbetatail_s.hoc to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/contents/NEURONcode/mdbetatail_s.hoc\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /afterdischarge-Prescott.sedml\ncreating dataset /afterdischarge-Prescott.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-2b0e6138-b90c45a6-f42e-99bca8-56ed39, chunk_size: (2, 1001)\ncreating dataset /afterdischarge-Prescott.sedml/report, shape: (8, 1001), type: float64\ndataset created, uuid: d-2b0e6138-b90c45a6-cec6-48283d-bf0f70, chunk_size: (8, 1001)\ncreating attribute combineArchiveLocation in /afterdischarge-Prescott.sedml\ncreating attribute uri in /afterdischarge-Prescott.sedml\ncreating attribute _type in /afterdischarge-Prescott.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /afterdischarge-Prescott.sedml/plot\ncreating attribute sedmlDataSetIds in /afterdischarge-Prescott.sedml/plot\ncreating attribute sedmlDataSetLabels in /afterdischarge-Prescott.sedml/plot\ncreating attribute sedmlDataSetNames in /afterdischarge-Prescott.sedml/plot\ncreating attribute sedmlDataSetShapes in /afterdischarge-Prescott.sedml/plot\ncreating attribute sedmlId in /afterdischarge-Prescott.sedml/plot\ncreating attribute uri in /afterdischarge-Prescott.sedml/plot\ncreating attribute _type in /afterdischarge-Prescott.sedml/report\ncreating attribute sedmlDataSetDataTypes in /afterdischarge-Prescott.sedml/report\ncreating attribute sedmlDataSetIds in /afterdischarge-Prescott.sedml/report\ncreating attribute sedmlDataSetLabels in /afterdischarge-Prescott.sedml/report\ncreating attribute sedmlDataSetNames in /afterdischarge-Prescott.sedml/report\ncreating attribute sedmlDataSetShapes in /afterdischarge-Prescott.sedml/report\ncreating attribute sedmlId in /afterdischarge-Prescott.sedml/report\ncreating attribute sedmlName in /afterdischarge-Prescott.sedml/report\ncreating attribute uri in /afterdischarge-Prescott.sedml/report\ncreate_links: /\ngot link: afterdischarge-Prescott.sedml\ncreate_links: /afterdischarge-Prescott.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /afterdischarge-Prescott.sedml/plot to tgt: /afterdischarge-Prescott.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /afterdischarge-Prescott.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /afterdischarge-Prescott.sedml/plot\nwrite_dataset src: /afterdischarge-Prescott.sedml/report to tgt: /afterdischarge-Prescott.sedml/report, shape: (8, 1001), type: float64\niterating over chunks for /afterdischarge-Prescott.sedml/report\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /afterdischarge-Prescott.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42acd8a14a834cbf3e0d\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 66%)\n  adding: outputs/afterdischarge-Prescott.sedml/ (stored 0%)\n  adding: outputs/afterdischarge-Prescott.sedml/plot.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 25%)\n  adding: rawLog.txt (deflated 82%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 72.3 KiB/98.7 KiB (990.7 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/output.zip\nCompleted 72.3 KiB/98.7 KiB (990.7 KiB/s) with 3 file(s) remaining\rCompleted 82.1 KiB/98.7 KiB (807.6 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/rawLog.txt\nCompleted 82.1 KiB/98.7 KiB (807.6 KiB/s) with 2 file(s) remaining\rCompleted 91.7 KiB/98.7 KiB (795.6 KiB/s) with 2 file(s) remaining\rupload: outputs/afterdischarge-Prescott.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/outputs/afterdischarge-Prescott.sedml/plot.pdf\nCompleted 91.7 KiB/98.7 KiB (795.6 KiB/s) with 1 file(s) remaining\rCompleted 98.7 KiB/98.7 KiB (810.5 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/outputs/plots.zip\nCompleted 82.0 KiB/82.0 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/outputs/reports.h5\nCompleted 2.3 KiB/2.3 KiB (40.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42acd8a14a834cbf3e0d/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}