{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_time"},{"status":"SUCCEEDED","id":"data_set_egf"},{"status":"SUCCEEDED","id":"data_set_erk"},{"status":"SUCCEEDED","id":"data_set_nfkb"},{"status":"SUCCEEDED","id":"data_set_tnfa"}],"duration":0.055682,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_egf"},{"status":"SUCCEEDED","id":"curve_tnfa"},{"status":"SUCCEEDED","id":"curve_erk"},{"status":"SUCCEEDED","id":"curve_nfkb"}],"duration":0.181978,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"Figure_4a"}],"tasks":[{"simulatorDetails":[{"value":"trace","key":"method"},{"value":["-m 20","-u synchronous"],"key":"arguments"}],"algorithm":"KISAO_0000449","duration":1.16468,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `model` may be invalid.\r\n  - The model file `/tmp/tmp078piotw.xml` may be invalid.\r\n    - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n       The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n      Reference: L3V1 Section 4.5\r\n       The <compartment> 'main' has no discernable units.\r\n      \u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":1.509199,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  simulation.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 5 data sets\r\n    Plots (1):\r\n      Figure_4a: 4 curves\r\n\r\nExecuting SED-ML file 1: simulation.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `Figure_4a`\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: `Figure_4a` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"simulation.sedml"}],"duration":1.771266,"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 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    431      0 --:--:-- --:--:-- --:--:--   431\n\r100 61882  100 61882    0     0   134k      0 --:--:-- --:--:-- --:--:--  134k\n\n\u001b[0;36m============================================= Executing COMBINE archive =============================================\u001b[0m\nINFO:    Using cached SIF image\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n  - Model `model` may be invalid.\r\n    - The model file `BIOMD0000000562_url.xml` may be invalid.\r\n      - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n         The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n        Reference: L3V1 Section 4.5\r\n         The <compartment> 'main' has no discernable units.\r\n        \r\n    - The changes of the model may be invalid.\r\n      - Change 1 may be invalid.\r\n        - XPath could not be validated.\r\n  - Data generator `data_generator_egf` may be invalid.\r\n    - Variable `var_egf` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_generator_erk` may be invalid.\r\n    - Variable `var_erk` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_generator_nfkb` may be invalid.\r\n    - Variable `var_nfkb` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_generator_tnfa` may be invalid.\r\n    - Variable `var_tnfa` may be invalid.\r\n      - XPath could not be validated.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n  - The SED-ML file at location `./simulation.sedml` may be invalid.\r\n    - Model `model` may be invalid.\r\n      - The model file `BIOMD0000000562_url.xml` may be invalid.\r\n        - In situations where a mathematical expression refers to a compartment, species or parameter, it is necessary to know the units of the object to establish unit consistency. In models where the units of an object have not been declared, libSBML does not yet have the functionality to accurately verify the consistency of the units in mathematical expressions referring to that object. \r\n           The units of the <compartment> 'main' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - If neither the attribute 'units' nor the attribute 'spatialDimensions' on a Compartment object is set, the unit associated with that compartment's size is undefined.\r\n          Reference: L3V1 Section 4.5\r\n           The <compartment> 'main' has no discernable units.\r\n          \r\n      - The changes of the model may be invalid.\r\n        - Change 1 may be invalid.\r\n          - XPath could not be validated.\r\n    - Data generator `data_generator_egf` may be invalid.\r\n      - Variable `var_egf` may be invalid.\r\n        - XPath could not be validated.\r\n    - Data generator `data_generator_erk` may be invalid.\r\n      - Variable `var_erk` may be invalid.\r\n        - XPath could not be validated.\r\n    - Data generator `data_generator_nfkb` may be invalid.\r\n      - Variable `var_nfkb` may be invalid.\r\n        - XPath could not be validated.\r\n    - Data generator `data_generator_tnfa` may be invalid.\r\n      - Variable `var_tnfa` may be invalid.\r\n        - XPath could not be validated.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n  - Model `model` may be invalid.\r\n    - The changes of the model may be invalid.\r\n      - Change 1 may be invalid.\r\n        - XPath could not be validated.\r\n  - Data generator `data_generator_egf` may be invalid.\r\n    - Variable `var_egf` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_generator_erk` may be invalid.\r\n    - Variable `var_erk` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_generator_nfkb` may be invalid.\r\n    - Variable `var_nfkb` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_generator_tnfa` may be invalid.\r\n    - Variable `var_tnfa` may be invalid.\r\n      - XPath could not be validated.\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 results ==================================================\u001b[0m\ncreating group /simulation.sedml\ncreating dataset /simulation.sedml/Figure_4a, shape: (5, 21), type: float64\ndataset created, uuid: d-2f41ea42-ddc0186d-d8ee-0c5126-ca8271, chunk_size: (5, 21)\ncreating dataset /simulation.sedml/report, shape: (5, 21), type: float64\ndataset created, uuid: d-2f41ea42-ddc0186d-0907-6cd6e8-09aa35, chunk_size: (5, 21)\ncreating attribute combineArchiveLocation in /simulation.sedml\ncreating attribute uri in /simulation.sedml\ncreating attribute _type in /simulation.sedml/Figure_4a\ncreating attribute sedmlDataSetDataTypes in /simulation.sedml/Figure_4a\ncreating attribute sedmlDataSetIds in /simulation.sedml/Figure_4a\ncreating attribute sedmlDataSetLabels in /simulation.sedml/Figure_4a\ncreating attribute sedmlDataSetNames in /simulation.sedml/Figure_4a\ncreating attribute sedmlDataSetShapes in /simulation.sedml/Figure_4a\ncreating attribute sedmlId in /simulation.sedml/Figure_4a\ncreating attribute sedmlName in /simulation.sedml/Figure_4a\ncreating attribute uri in /simulation.sedml/Figure_4a\ncreating attribute _type in /simulation.sedml/report\ncreating attribute sedmlDataSetDataTypes in /simulation.sedml/report\ncreating attribute sedmlDataSetIds in /simulation.sedml/report\ncreating attribute sedmlDataSetLabels in /simulation.sedml/report\ncreating attribute sedmlDataSetNames in /simulation.sedml/report\ncreating attribute sedmlDataSetShapes in /simulation.sedml/report\ncreating attribute sedmlId in /simulation.sedml/report\ncreating attribute uri in /simulation.sedml/report\ncreate_links: /\ngot link: simulation.sedml\ncreate_links: /simulation.sedml\ngot link: Figure_4a\ngot link: report\nwrite_dataset src: /simulation.sedml/Figure_4a to tgt: /simulation.sedml/Figure_4a, shape: (5, 21), type: float64\niterating over chunks for /simulation.sedml/Figure_4a\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 21, 1))\ndone with dataload for /simulation.sedml/Figure_4a\nwrite_dataset src: /simulation.sedml/report to tgt: /simulation.sedml/report, shape: (5, 21), type: float64\niterating over chunks for /simulation.sedml/report\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 21, 1))\ndone with dataload for /simulation.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/61fea485f499ccf25faafc50\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/simulation.sedml/ (stored 0%)\n  adding: outputs/simulation.sedml/Figure_4a.pdf (deflated 35%)\n  adding: outputs/log.yml (deflated 79%)\n  adding: outputs/reports.h5 (deflated 94%)\n  adding: rawLog.txt (deflated 80%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nupload: ./jsbml.log to s3://files.biosimulations.org/simulations/61fea485f499ccf25faafc50/jsbml.log\nCompleted 0 Bytes/39.0 KiB (0 Bytes/s) with 4 file(s) remaining\rCompleted 12.8 KiB/39.0 KiB (93.3 KiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/61fea485f499ccf25faafc50/output.zip\nCompleted 12.8 KiB/39.0 KiB (93.3 KiB/s) with 3 file(s) remaining\rCompleted 21.7 KiB/39.0 KiB (154.9 KiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/61fea485f499ccf25faafc50/rawLog.txt\nCompleted 21.7 KiB/39.0 KiB (154.9 KiB/s) with 2 file(s) remaining\rCompleted 28.4 KiB/39.0 KiB (198.2 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/61fea485f499ccf25faafc50/outputs/plots.zip\nCompleted 28.4 KiB/39.0 KiB (198.2 KiB/s) with 1 file(s) remaining\rCompleted 39.0 KiB/39.0 KiB (251.2 KiB/s) with 1 file(s) remaining\rupload: outputs/simulation.sedml/Figure_4a.pdf to s3://files.biosimulations.org/simulations/61fea485f499ccf25faafc50/outputs/simulation.sedml/Figure_4a.pdf\nCompleted 24.1 KiB/24.1 KiB (206.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/61fea485f499ccf25faafc50/outputs/reports.h5\nCompleted 8.5 KiB/8.5 KiB (92.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/61fea485f499ccf25faafc50/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\n\u001b[0;32mProcess and upload the outputs of the simulation run.....Succeeded\nPost the Metadata to the API.....Succeeded\nProcess the Metadata in the combine archive.....Succeeded\nPost the logs to the API.....Succeeded\nRetrieve the logs of the simulation run.....Succeeded\nPost thumbnails to the API.....Succeeded\nCreate thumbnails from the images specified in the manifest.....Succeeded\nRead the manifest and post the files to the API.....Succeeded\nExtract the files in the combine archive.....Succeeded\nProcess the manifest file in the combine archive.....Succeeded\nPost the SED-ML file to the API.....Succeeded\nProcess the SED-ML file in the combine archive.....Succeeded\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}