{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_CA"},{"status":"SUCCEEDED","id":"data_set_HH"},{"status":"SUCCEEDED","id":"data_set_HNAP"},{"status":"SUCCEEDED","id":"data_set_MLVA"},{"status":"SUCCEEDED","id":"data_set_NHVK"},{"status":"SUCCEEDED","id":"data_set_NK"},{"status":"SUCCEEDED","id":"data_set_V"}],"duration":0.122175,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.245329,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"600.0","key":"total"},{"value":"rungekutta","key":"meth"},{"value":"0.2","key":"dt"},{"value":"0.0","key":"t0"},{"value":"3","key":"njmp"}],"algorithm":"KISAO_0000032","duration":0.178964,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.68356,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  xpp/bifurcation.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: xpp/bifurcation.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":"xpp/bifurcation.sedml"}],"duration":1.1723,"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    458      0 --:--:-- --:--:-- --:--:--   458\n\r100 74269  100 74269    0     0   175k      0 --:--:-- --:--:-- --:--:--  175k\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.md      \n  inflating: contents/README.html    \n  inflating: contents/parameters.m   \n  inflating: contents/ET.m           \n  inflating: contents/xpp/bifurcation.ode  \n  inflating: contents/ME-PCM/README.md  \n  inflating: contents/ME-PCM/makefile  \n  inflating: contents/ME-PCM/uq_parameters.h  \n  inflating: contents/ME-PCM/uq_ET.c  \n  inflating: contents/ME-PCM/uq_ETCell.h  \n  inflating: contents/ME-PCM/abscissa.c  \n  inflating: contents/ME-PCM/uq_processTrace.c  \n  inflating: contents/ME-PCM/readTrace.c  \n  inflating: contents/ME-PCM/sample.c  \n  inflating: contents/xpp/bifurcation.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/screenshot.png  \n  inflating: contents/manifest.xml   \nCompleted 5.5 KiB/168.2 KiB (54.2 KiB/s) with 18 file(s) remaining\rupload: contents/ET.m to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/ET.m\nCompleted 5.5 KiB/168.2 KiB (54.2 KiB/s) with 17 file(s) remaining\rCompleted 6.8 KiB/168.2 KiB (54.9 KiB/s) with 17 file(s) remaining\rupload: contents/ME-PCM/README.md to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/ME-PCM/README.md\nCompleted 6.8 KiB/168.2 KiB (54.9 KiB/s) with 16 file(s) remaining\rCompleted 7.0 KiB/168.2 KiB (53.4 KiB/s) with 16 file(s) remaining\rupload: contents/ME-PCM/uq_ETCell.h to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/ME-PCM/uq_ETCell.h\nCompleted 7.0 KiB/168.2 KiB (53.4 KiB/s) with 15 file(s) remaining\rCompleted 10.7 KiB/168.2 KiB (74.4 KiB/s) with 15 file(s) remaining\rupload: contents/ME-PCM/uq_processTrace.c to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/ME-PCM/uq_processTrace.c\nCompleted 10.7 KiB/168.2 KiB (74.4 KiB/s) with 14 file(s) remaining\rCompleted 12.3 KiB/168.2 KiB (84.8 KiB/s) with 14 file(s) remaining\rupload: contents/ME-PCM/uq_parameters.h to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/ME-PCM/uq_parameters.h\nCompleted 12.3 KiB/168.2 KiB (84.8 KiB/s) with 13 file(s) remaining\rCompleted 16.2 KiB/168.2 KiB (101.7 KiB/s) with 13 file(s) remaining\rupload: contents/README.html to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/README.html\nCompleted 16.2 KiB/168.2 KiB (101.7 KiB/s) with 12 file(s) remaining\rCompleted 17.8 KiB/168.2 KiB (109.9 KiB/s) with 12 file(s) remaining\rupload: contents/README.md to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/README.md\nCompleted 17.8 KiB/168.2 KiB (109.9 KiB/s) with 11 file(s) remaining\rCompleted 114.8 KiB/168.2 KiB (663.1 KiB/s) with 11 file(s) remaining\rupload: contents/ME-PCM/abscissa.c to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/ME-PCM/abscissa.c\nCompleted 114.8 KiB/168.2 KiB (663.1 KiB/s) with 10 file(s) remaining\rCompleted 125.7 KiB/168.2 KiB (707.0 KiB/s) with 10 file(s) remaining\rupload: contents/screenshot.png to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/screenshot.png\nCompleted 125.7 KiB/168.2 KiB (707.0 KiB/s) with 9 file(s) remaining\rCompleted 127.7 KiB/168.2 KiB (711.3 KiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/manifest.xml\nCompleted 127.7 KiB/168.2 KiB (711.3 KiB/s) with 8 file(s) remaining\rCompleted 131.0 KiB/168.2 KiB (708.5 KiB/s) with 8 file(s) remaining\rupload: contents/xpp/bifurcation.ode to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/xpp/bifurcation.ode\nCompleted 131.0 KiB/168.2 KiB (708.5 KiB/s) with 7 file(s) remaining\rCompleted 140.9 KiB/168.2 KiB (738.1 KiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/metadata.rdf\nCompleted 140.9 KiB/168.2 KiB (738.1 KiB/s) with 6 file(s) remaining\rCompleted 145.6 KiB/168.2 KiB (746.5 KiB/s) with 6 file(s) remaining\rupload: contents/ME-PCM/uq_ET.c to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/ME-PCM/uq_ET.c\nCompleted 145.6 KiB/168.2 KiB (746.5 KiB/s) with 5 file(s) remaining\rCompleted 153.0 KiB/168.2 KiB (712.5 KiB/s) with 5 file(s) remaining\rupload: contents/xpp/bifurcation.sedml to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/xpp/bifurcation.sedml\nCompleted 153.0 KiB/168.2 KiB (712.5 KiB/s) with 4 file(s) remaining\rCompleted 154.6 KiB/168.2 KiB (711.7 KiB/s) with 4 file(s) remaining\rupload: contents/parameters.m to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/parameters.m\nCompleted 154.6 KiB/168.2 KiB (711.7 KiB/s) with 3 file(s) remaining\rCompleted 155.2 KiB/168.2 KiB (703.2 KiB/s) with 3 file(s) remaining\rupload: contents/ME-PCM/readTrace.c to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/ME-PCM/readTrace.c\nCompleted 155.2 KiB/168.2 KiB (703.2 KiB/s) with 2 file(s) remaining\rCompleted 167.8 KiB/168.2 KiB (750.5 KiB/s) with 2 file(s) remaining\rupload: contents/ME-PCM/sample.c to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/ME-PCM/sample.c\nCompleted 167.8 KiB/168.2 KiB (750.5 KiB/s) with 1 file(s) remaining\rCompleted 168.2 KiB/168.2 KiB (668.2 KiB/s) with 1 file(s) remaining\rupload: contents/ME-PCM/makefile to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/contents/ME-PCM/makefile\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /xpp\ncreating group /xpp/bifurcation.sedml\ncreating dataset /xpp/bifurcation.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-cdc038fc-3bc63a26-c587-ce92e8-7449b0, chunk_size: (2, 1001)\ncreating dataset /xpp/bifurcation.sedml/report, shape: (8, 1001), type: float64\ndataset created, uuid: d-cdc038fc-3bc63a26-2255-0bf316-107d67, chunk_size: (8, 1001)\ncreating attribute combineArchiveLocation in /xpp\ncreating attribute uri in /xpp\ncreating attribute combineArchiveLocation in /xpp/bifurcation.sedml\ncreating attribute uri in /xpp/bifurcation.sedml\ncreating attribute _type in /xpp/bifurcation.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /xpp/bifurcation.sedml/plot\ncreating attribute sedmlDataSetIds in /xpp/bifurcation.sedml/plot\ncreating attribute sedmlDataSetLabels in /xpp/bifurcation.sedml/plot\ncreating attribute sedmlDataSetNames in /xpp/bifurcation.sedml/plot\ncreating attribute sedmlDataSetShapes in /xpp/bifurcation.sedml/plot\ncreating attribute sedmlId in /xpp/bifurcation.sedml/plot\ncreating attribute uri in /xpp/bifurcation.sedml/plot\ncreating attribute _type in /xpp/bifurcation.sedml/report\ncreating attribute sedmlDataSetDataTypes in /xpp/bifurcation.sedml/report\ncreating attribute sedmlDataSetIds in /xpp/bifurcation.sedml/report\ncreating attribute sedmlDataSetLabels in /xpp/bifurcation.sedml/report\ncreating attribute sedmlDataSetNames in /xpp/bifurcation.sedml/report\ncreating attribute sedmlDataSetShapes in /xpp/bifurcation.sedml/report\ncreating attribute sedmlId in /xpp/bifurcation.sedml/report\ncreating attribute sedmlName in /xpp/bifurcation.sedml/report\ncreating attribute uri in /xpp/bifurcation.sedml/report\ncreate_links: /\ngot link: xpp\ncreate_links: /xpp\ngot link: bifurcation.sedml\ncreate_links: /xpp/bifurcation.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /xpp/bifurcation.sedml/plot to tgt: /xpp/bifurcation.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /xpp/bifurcation.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /xpp/bifurcation.sedml/plot\nwrite_dataset src: /xpp/bifurcation.sedml/report to tgt: /xpp/bifurcation.sedml/report, shape: (8, 1001), type: float64\niterating over chunks for /xpp/bifurcation.sedml/report\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /xpp/bifurcation.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42beb50991044c79ae43\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 66%)\n  adding: outputs/xpp/ (stored 0%)\n  adding: outputs/xpp/bifurcation.sedml/ (stored 0%)\n  adding: outputs/xpp/bifurcation.sedml/plot.pdf (deflated 34%)\n  adding: outputs/reports.h5 (deflated 25%)\n  adding: rawLog.txt (deflated 82%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 71.1 KiB/93.8 KiB (881.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/output.zip\nCompleted 71.1 KiB/93.8 KiB (881.3 KiB/s) with 3 file(s) remaining\rCompleted 76.0 KiB/93.8 KiB (771.3 KiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/outputs/plots.zip\nCompleted 76.0 KiB/93.8 KiB (771.3 KiB/s) with 2 file(s) remaining\rCompleted 83.6 KiB/93.8 KiB (806.7 KiB/s) with 2 file(s) remaining\rupload: outputs/xpp/bifurcation.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/outputs/xpp/bifurcation.sedml/plot.pdf\nCompleted 83.6 KiB/93.8 KiB (806.7 KiB/s) with 1 file(s) remaining\rCompleted 93.8 KiB/93.8 KiB (646.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/rawLog.txt\nCompleted 83.4 KiB/83.4 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/outputs/reports.h5\nCompleted 2.3 KiB/2.3 KiB (40.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42beb50991044c79ae43/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.\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 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"}