{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_A"},{"status":"SUCCEEDED","id":"data_set_M"},{"status":"SUCCEEDED","id":"data_set_P"},{"status":"SUCCEEDED","id":"data_set_PC"},{"status":"SUCCEEDED","id":"data_set_R"}],"duration":0.067246,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"}],"tasks":[{"simulatorDetails":[{"value":"stiff","key":"meth"},{"value":"0.0","key":"t0"},{"value":"20.0","key":"total"},{"value":"0.05","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000668","duration":0.074958,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.230166,"output":"Archive contains 3 SED-ML documents with 3 models, 3 simulations, 3 tasks, 3 reports, and 0 plots:\r\n  NNF.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 6 data sets\r\n  PNF.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 6 data sets\r\n  SNF.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 4 data sets\r\n\r\nExecuting SED-ML file 1: NNF.sedml ...\r\n  Found 1 tasks and 1 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 1 outputs ...\r\n      Generating output 1: `report` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"NNF.sedml"},{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_A"},{"status":"SUCCEEDED","id":"data_set_M"},{"status":"SUCCEEDED","id":"data_set_P"},{"status":"SUCCEEDED","id":"data_set_PC"},{"status":"SUCCEEDED","id":"data_set_R"}],"duration":0.061123,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"}],"tasks":[{"simulatorDetails":[{"value":"stiff","key":"meth"},{"value":"0.0","key":"t0"},{"value":"20.0","key":"total"},{"value":"0.05","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000668","duration":0.061423,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.218876,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 1 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 2: PNF.sedml ...\r\n  Found 1 tasks and 1 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 1 outputs ...\r\n      Generating output 1: `report` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"PNF.sedml"},{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_M"},{"status":"SUCCEEDED","id":"data_set_P"},{"status":"SUCCEEDED","id":"data_set_PC"}],"duration":0.053152,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"}],"tasks":[{"simulatorDetails":[{"value":"stiff","key":"meth"},{"value":"0.0","key":"t0"},{"value":"20.0","key":"total"},{"value":"0.05","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000668","duration":0.056916,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.204732,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 1 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 3: SNF.sedml ...\r\n  Found 1 tasks and 1 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 1 outputs ...\r\n      Generating output 1: `report` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"SNF.sedml"}],"duration":1.091192,"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    471      0 --:--:-- --:--:-- --:--:--   471\n\r100  662k  100  662k    0     0  1549k      0 --:--:-- --:--:-- --:--:-- 1549k\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 1 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 3 SED documents:\n  SED documents (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n  Tasks (3):\n    Succeeded: 3\n    Skipped: 0\n    Failed: 0\n  Outputs (3):\n    Succeeded: 3\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/NNF.c          \n  inflating: contents/SNF.m          \n  inflating: contents/NNF.m          \n  inflating: contents/PNF.m          \n  inflating: contents/SNF.ode        \n  inflating: contents/Sim_Clock_Model.nb  \n  inflating: contents/PNF.xml        \n  inflating: contents/SNF.c          \n  inflating: contents/README.txt     \n  inflating: contents/PNF.ode        \n  inflating: contents/PNF.c          \n  inflating: contents/NNF.xml        \n  inflating: contents/SNF.xml        \n  inflating: contents/NNF.ode        \n  inflating: contents/NNF.sedml      \n  inflating: contents/PNF.sedml      \n  inflating: contents/SNF.sedml      \n  inflating: contents/metadata.rdf   \n  inflating: contents/article-figures/PMC3542529/msb201262-f1.jpg  \n  inflating: contents/article-figures/PMC3542529/msb201262-f2.jpg  \n  inflating: contents/article-figures/PMC3542529/msb201262-f3.jpg  \n  inflating: contents/article-figures/PMC3542529/msb201262-f4.jpg  \n  inflating: contents/article-figures/PMC3542529/msb201262-f5.jpg  \n  inflating: contents/article-figures/PMC3542529/msb201262-f6.jpg  \n  inflating: contents/manifest.xml   \nCompleted 4.0 KiB/941.0 KiB (41.6 KiB/s) with 25 file(s) remaining\rupload: contents/NNF.c to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/NNF.c\nCompleted 4.0 KiB/941.0 KiB (41.6 KiB/s) with 24 file(s) remaining\rCompleted 5.4 KiB/941.0 KiB (41.4 KiB/s) with 24 file(s) remaining\rupload: contents/PNF.ode to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/PNF.ode\nCompleted 5.4 KiB/941.0 KiB (41.4 KiB/s) with 23 file(s) remaining\rCompleted 9.4 KiB/941.0 KiB (70.9 KiB/s) with 23 file(s) remaining\rupload: contents/PNF.sedml to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/PNF.sedml\nCompleted 9.4 KiB/941.0 KiB (70.9 KiB/s) with 22 file(s) remaining\rCompleted 32.1 KiB/941.0 KiB (226.3 KiB/s) with 22 file(s) remaining\rupload: contents/PNF.xml to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/PNF.xml\nCompleted 32.1 KiB/941.0 KiB (226.3 KiB/s) with 21 file(s) remaining\rCompleted 33.5 KiB/941.0 KiB (228.6 KiB/s) with 21 file(s) remaining\rupload: contents/NNF.ode to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/NNF.ode\nCompleted 33.5 KiB/941.0 KiB (228.6 KiB/s) with 20 file(s) remaining\rCompleted 36.5 KiB/941.0 KiB (238.3 KiB/s) with 20 file(s) remaining\rupload: contents/SNF.sedml to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/SNF.sedml\nCompleted 36.5 KiB/941.0 KiB (238.3 KiB/s) with 19 file(s) remaining\rCompleted 38.8 KiB/941.0 KiB (247.3 KiB/s) with 19 file(s) remaining\rupload: contents/SNF.c to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/SNF.c\nCompleted 38.8 KiB/941.0 KiB (247.3 KiB/s) with 18 file(s) remaining\rCompleted 42.8 KiB/941.0 KiB (270.4 KiB/s) with 18 file(s) remaining\rupload: contents/NNF.sedml to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/NNF.sedml\nCompleted 42.8 KiB/941.0 KiB (270.4 KiB/s) with 17 file(s) remaining\rCompleted 60.5 KiB/941.0 KiB (279.8 KiB/s) with 17 file(s) remaining\rupload: contents/SNF.xml to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/SNF.xml\nCompleted 60.5 KiB/941.0 KiB (279.8 KiB/s) with 16 file(s) remaining\rCompleted 199.5 KiB/941.0 KiB (899.0 KiB/s) with 16 file(s) remaining\rCompleted 313.0 KiB/941.0 KiB (1.4 MiB/s) with 16 file(s) remaining  \rupload: contents/article-figures/PMC3542529/msb201262-f3.jpg to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/article-figures/PMC3542529/msb201262-f3.jpg\nCompleted 313.0 KiB/941.0 KiB (1.4 MiB/s) with 15 file(s) remaining\rCompleted 448.8 KiB/941.0 KiB (2.0 MiB/s) with 15 file(s) remaining\rupload: contents/article-figures/PMC3542529/msb201262-f2.jpg to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/article-figures/PMC3542529/msb201262-f2.jpg\nCompleted 448.8 KiB/941.0 KiB (2.0 MiB/s) with 14 file(s) remaining\rupload: contents/article-figures/PMC3542529/msb201262-f1.jpg to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/article-figures/PMC3542529/msb201262-f1.jpg\nCompleted 448.8 KiB/941.0 KiB (2.0 MiB/s) with 13 file(s) remaining\rCompleted 452.2 KiB/941.0 KiB (1.9 MiB/s) with 13 file(s) remaining\rCompleted 539.3 KiB/941.0 KiB (2.2 MiB/s) with 13 file(s) remaining\rupload: contents/article-figures/PMC3542529/msb201262-f5.jpg to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/article-figures/PMC3542529/msb201262-f5.jpg\nCompleted 539.3 KiB/941.0 KiB (2.2 MiB/s) with 12 file(s) remaining\rCompleted 643.1 KiB/941.0 KiB (2.6 MiB/s) with 12 file(s) remaining\rupload: contents/Sim_Clock_Model.nb to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/Sim_Clock_Model.nb\nCompleted 643.1 KiB/941.0 KiB (2.6 MiB/s) with 11 file(s) remaining\rCompleted 788.1 KiB/941.0 KiB (3.1 MiB/s) with 11 file(s) remaining\rupload: contents/article-figures/PMC3542529/msb201262-f4.jpg to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/article-figures/PMC3542529/msb201262-f4.jpg\nCompleted 788.1 KiB/941.0 KiB (3.1 MiB/s) with 10 file(s) remaining\rupload: contents/SNF.m to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/SNF.m\nCompleted 788.1 KiB/941.0 KiB (3.1 MiB/s) with 9 file(s) remaining\rCompleted 789.4 KiB/941.0 KiB (3.1 MiB/s) with 9 file(s) remaining\rupload: contents/SNF.ode to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/SNF.ode\nCompleted 789.4 KiB/941.0 KiB (3.1 MiB/s) with 8 file(s) remaining\rCompleted 789.9 KiB/941.0 KiB (2.8 MiB/s) with 8 file(s) remaining\rupload: contents/README.txt to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/README.txt\nCompleted 789.9 KiB/941.0 KiB (2.8 MiB/s) with 7 file(s) remaining\rCompleted 800.5 KiB/941.0 KiB (2.7 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/metadata.rdf\nCompleted 800.5 KiB/941.0 KiB (2.7 MiB/s) with 6 file(s) remaining\rCompleted 804.2 KiB/941.0 KiB (2.7 MiB/s) with 6 file(s) remaining\rupload: contents/PNF.m to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/PNF.m\nCompleted 804.2 KiB/941.0 KiB (2.7 MiB/s) with 5 file(s) remaining\rCompleted 807.9 KiB/941.0 KiB (2.5 MiB/s) with 5 file(s) remaining\rupload: contents/NNF.m to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/NNF.m\nCompleted 807.9 KiB/941.0 KiB (2.5 MiB/s) with 4 file(s) remaining\rCompleted 831.7 KiB/941.0 KiB (2.6 MiB/s) with 4 file(s) remaining\rupload: contents/NNF.xml to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/NNF.xml\nCompleted 831.7 KiB/941.0 KiB (2.6 MiB/s) with 3 file(s) remaining\rCompleted 935.1 KiB/941.0 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: contents/article-figures/PMC3542529/msb201262-f6.jpg to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/article-figures/PMC3542529/msb201262-f6.jpg\nCompleted 935.1 KiB/941.0 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 938.2 KiB/941.0 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: contents/PNF.c to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/PNF.c\nCompleted 938.2 KiB/941.0 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 941.0 KiB/941.0 KiB (2.6 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/contents/manifest.xml\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /NNF.sedml\ncreating dataset /NNF.sedml/report, shape: (6, 401), type: float64\ndataset created, uuid: d-470ffccf-d0bee700-c1d9-c3fc9a-8cb3ea, chunk_size: (6, 401)\ncreating group /PNF.sedml\ncreating dataset /PNF.sedml/report, shape: (6, 401), type: float64\ndataset created, uuid: d-470ffccf-d0bee700-8403-fdcb40-e6c61c, chunk_size: (6, 401)\ncreating group /SNF.sedml\ncreating dataset /SNF.sedml/report, shape: (4, 401), type: float64\ndataset created, uuid: d-470ffccf-d0bee700-d5d6-c32505-0e3612, chunk_size: (4, 401)\ncreating attribute combineArchiveLocation in /NNF.sedml\ncreating attribute uri in /NNF.sedml\ncreating attribute _type in /NNF.sedml/report\ncreating attribute sedmlDataSetDataTypes in /NNF.sedml/report\ncreating attribute sedmlDataSetIds in /NNF.sedml/report\ncreating attribute sedmlDataSetLabels in /NNF.sedml/report\ncreating attribute sedmlDataSetNames in /NNF.sedml/report\ncreating attribute sedmlDataSetShapes in /NNF.sedml/report\ncreating attribute sedmlId in /NNF.sedml/report\ncreating attribute sedmlName in /NNF.sedml/report\ncreating attribute uri in /NNF.sedml/report\ncreating attribute combineArchiveLocation in /PNF.sedml\ncreating attribute uri in /PNF.sedml\ncreating attribute _type in /PNF.sedml/report\ncreating attribute sedmlDataSetDataTypes in /PNF.sedml/report\ncreating attribute sedmlDataSetIds in /PNF.sedml/report\ncreating attribute sedmlDataSetLabels in /PNF.sedml/report\ncreating attribute sedmlDataSetNames in /PNF.sedml/report\ncreating attribute sedmlDataSetShapes in /PNF.sedml/report\ncreating attribute sedmlId in /PNF.sedml/report\ncreating attribute sedmlName in /PNF.sedml/report\ncreating attribute uri in /PNF.sedml/report\ncreating attribute combineArchiveLocation in /SNF.sedml\ncreating attribute uri in /SNF.sedml\ncreating attribute _type in /SNF.sedml/report\ncreating attribute sedmlDataSetDataTypes in /SNF.sedml/report\ncreating attribute sedmlDataSetIds in /SNF.sedml/report\ncreating attribute sedmlDataSetLabels in /SNF.sedml/report\ncreating attribute sedmlDataSetNames in /SNF.sedml/report\ncreating attribute sedmlDataSetShapes in /SNF.sedml/report\ncreating attribute sedmlId in /SNF.sedml/report\ncreating attribute sedmlName in /SNF.sedml/report\ncreating attribute uri in /SNF.sedml/report\ncreate_links: /\ngot link: NNF.sedml\ngot link: PNF.sedml\ngot link: SNF.sedml\ncreate_links: /NNF.sedml\ngot link: report\ncreate_links: /PNF.sedml\ngot link: report\ncreate_links: /SNF.sedml\ngot link: report\nwrite_dataset src: /NNF.sedml/report to tgt: /NNF.sedml/report, shape: (6, 401), type: float64\niterating over chunks for /NNF.sedml/report\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 401, 1))\ndone with dataload for /NNF.sedml/report\nwrite_dataset src: /PNF.sedml/report to tgt: /PNF.sedml/report, shape: (6, 401), type: float64\niterating over chunks for /PNF.sedml/report\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 401, 1))\ndone with dataload for /PNF.sedml/report\nwrite_dataset src: /SNF.sedml/report to tgt: /SNF.sedml/report, shape: (4, 401), type: float64\niterating over chunks for /SNF.sedml/report\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 401, 1))\ndone with dataload for /SNF.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42add8a14a834cbf3e18\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 81%)\n  adding: outputs/reports.h5 (deflated 45%)\n  adding: rawLog.txt (deflated 85%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 46.5 KiB/59.7 KiB (693.8 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/output.zip\nCompleted 46.5 KiB/59.7 KiB (693.8 KiB/s) with 1 file(s) remaining\rCompleted 59.7 KiB/59.7 KiB (658.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/rawLog.txt\nCompleted 78.3 KiB/78.3 KiB (602.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/outputs/reports.h5\nCompleted 4.7 KiB/4.7 KiB (88.2 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42add8a14a834cbf3e18/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess 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.\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.\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"}