{"status":"SUCCEEDED","exception":null,"skipReason":null,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m=================================================== Set up storage ==================================================\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 0 463 0 --:--:-- --:--:-- --:--:-- 464\n\r100 1512k 100 1512k 0 0 3185k 0 --:--:-- --:--:-- --:--:-- 3185k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO: Using cached SIF image\nTraceback (most recent call last):\n File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 247, in \n if not update_paths(args.path, args.scripts_dir, args.clear_args, args.extra_args):\n File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 213, in update_paths\n update_scripts(scripts_dir, new_path, clear_args, extra_args)\n File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 125, in update_scripts\n update_script(os.path.join(bin_dir, fn), new_path, clear_args, extra_args)\n File \"/home/opencor/OpenCOR/bin/../python/bin/set_python_path.py\", line 118, in update_script\n with open(script_filename, 'w') as f:\nOSError: [Errno 30] Read-only file system: '/home/opencor/OpenCOR/bin/../python/bin/biosimulators-utils'\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mCOMBINE/OMEX archive may be invalid.\n - The manifest does not include its parent COMBINE/OMEX archive. Manifests should include their parent COMBINE/OMEX archives.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n - Output `plot1` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n - Output `plot2` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n - Output `plot3` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n - Output `plot4` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n - Output `plot5` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n - Output `plot6` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\n - The SED-ML file at location `barberis_klipp_vanoni_alberghina_2007_Fig3.sedml` may be invalid.\n - Output `plot1` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n - Output `plot2` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n - Output `plot3` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n - Output `plot4` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n - Output `plot5` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\n - Output `plot6` may be invalid.\n - Some simulation tools will not be able to generate this output because it uses data from repeated tasks. Output for repeated tasks is an experimental feature of SED-ML, which is not officially supported.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\nArchive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 0 reports, and 6 plots:\n barberis_klipp_vanoni_alberghina_2007_Fig3.sedml:\n Tasks (2):\n repeatedTask\n task1\n Plots (6):\n plot1: 2 curves\n plot2: 2 curves\n plot3: 2 curves\n plot4: 2 curves\n plot5: 2 curves\n plot6: 2 curves\n\nExecuting SED-ML file 1: barberis_klipp_vanoni_alberghina_2007_Fig3.sedml ...\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 (2):\n Succeeded: 2\n Skipped: 0\n Failed: 0\n Outputs (6):\n Succeeded: 6\n Skipped: 0\n Failed: 0\n\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 6.4 KiB/6.4 KiB (34.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/rawLog.txt\nCompleted 15.7 KiB/15.7 KiB (219.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n adding: outputs/ (stored 0%)\n adding: outputs/log.yml (deflated 88%)\n adding: outputs/reports.h5 (deflated 34%)\n adding: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/ (stored 0%)\n adding: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3.pdf (deflated 29%)\n adding: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4.pdf (deflated 29%)\n adding: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5.pdf (deflated 32%)\n adding: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2.pdf (deflated 29%)\n adding: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1.pdf (deflated 30%)\n adding: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6.pdf (deflated 29%)\n adding: rawLog.txt (deflated 80%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 214.1 KiB/214.1 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/outputs/reports.h5\nCompleted 186.9 KiB/292.1 KiB (1.9 MiB/s) with 9 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/output.zip\nCompleted 186.9 KiB/292.1 KiB (1.9 MiB/s) with 8 file(s) remaining\rCompleted 196.4 KiB/292.1 KiB (1.3 MiB/s) with 8 file(s) remaining\rupload: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1.pdf to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1.pdf\nCompleted 196.4 KiB/292.1 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 204.4 KiB/292.1 KiB (1.3 MiB/s) with 7 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/rawLog.txt\nCompleted 204.4 KiB/292.1 KiB (1.3 MiB/s) with 6 file(s) remaining\rCompleted 213.1 KiB/292.1 KiB (1.3 MiB/s) with 6 file(s) remaining\rupload: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5.pdf to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5.pdf\nCompleted 213.1 KiB/292.1 KiB (1.3 MiB/s) with 5 file(s) remaining\rCompleted 223.2 KiB/292.1 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2.pdf to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2.pdf\nCompleted 223.2 KiB/292.1 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 232.8 KiB/292.1 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4.pdf to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4.pdf\nCompleted 232.8 KiB/292.1 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 272.5 KiB/292.1 KiB (1.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/outputs/plots.zip\nCompleted 272.5 KiB/292.1 KiB (1.3 MiB/s) with 2 file(s) remaining\rCompleted 282.4 KiB/292.1 KiB (1.2 MiB/s) with 2 file(s) remaining\rupload: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3.pdf to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3.pdf\nCompleted 282.4 KiB/292.1 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 292.1 KiB/292.1 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6.pdf to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/outputs/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive: archive.omex\n inflating: contents/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml \n inflating: contents/barberis_2007.ai \n inflating: contents/barberis_klipp_vanoni_alberghina_2007.cellml \n inflating: contents/barberis_2007.svg \n inflating: contents/barberis_2007.png \n inflating: contents/metadata.rdf \n inflating: contents/manifest.xml \nCompleted 256.0 KiB/2.5 MiB (3.2 MiB/s) with 7 file(s) remaining\rCompleted 512.0 KiB/2.5 MiB (5.2 MiB/s) with 7 file(s) remaining\rCompleted 768.0 KiB/2.5 MiB (7.0 MiB/s) with 7 file(s) remaining\rCompleted 1.0 MiB/2.5 MiB (9.1 MiB/s) with 7 file(s) remaining \rCompleted 1.2 MiB/2.5 MiB (11.0 MiB/s) with 7 file(s) remaining \rCompleted 1.5 MiB/2.5 MiB (12.8 MiB/s) with 7 file(s) remaining \rCompleted 1.8 MiB/2.5 MiB (14.8 MiB/s) with 7 file(s) remaining \rCompleted 2.0 MiB/2.5 MiB (16.1 MiB/s) with 7 file(s) remaining \rCompleted 2.0 MiB/2.5 MiB (14.7 MiB/s) with 7 file(s) remaining \rupload: contents/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/contents/barberis_klipp_vanoni_alberghina_2007_Fig3.sedml\nCompleted 2.0 MiB/2.5 MiB (14.7 MiB/s) with 6 file(s) remaining\rCompleted 2.0 MiB/2.5 MiB (13.6 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/contents/manifest.xml\nCompleted 2.0 MiB/2.5 MiB (13.6 MiB/s) with 5 file(s) remaining\rCompleted 2.0 MiB/2.5 MiB (13.4 MiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/contents/metadata.rdf\nCompleted 2.0 MiB/2.5 MiB (13.4 MiB/s) with 4 file(s) remaining\rCompleted 2.2 MiB/2.5 MiB (13.2 MiB/s) with 4 file(s) remaining\rupload: contents/barberis_2007.png to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/contents/barberis_2007.png\nCompleted 2.2 MiB/2.5 MiB (13.2 MiB/s) with 3 file(s) remaining\rCompleted 2.3 MiB/2.5 MiB (10.5 MiB/s) with 3 file(s) remaining\rupload: contents/barberis_klipp_vanoni_alberghina_2007.cellml to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/contents/barberis_klipp_vanoni_alberghina_2007.cellml\nCompleted 2.3 MiB/2.5 MiB (10.5 MiB/s) with 2 file(s) remaining\rCompleted 2.3 MiB/2.5 MiB (10.4 MiB/s) with 2 file(s) remaining\rupload: contents/barberis_2007.ai to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/contents/barberis_2007.ai\nCompleted 2.3 MiB/2.5 MiB (10.4 MiB/s) with 1 file(s) remaining\rCompleted 2.5 MiB/2.5 MiB (10.4 MiB/s) with 1 file(s) remaining\rupload: contents/barberis_2007.svg to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/contents/barberis_2007.svg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 13.5 KiB/13.5 KiB (182.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6261739190c6a195955782fb/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml\ncreating dataset /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1, shape: (4, 1, 1, 1401), type: float64\ndataset created, uuid: d-c2785d13-93b00844-c665-a4e3ec-d8bb63, chunk_size: (4, 1, 1, 1401)\ncreating dataset /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2, shape: (4, 1, 1, 1401), type: float64\ndataset created, uuid: d-c2785d13-93b00844-9511-1c63b0-b2e098, chunk_size: (4, 1, 1, 1401)\ncreating dataset /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3, shape: (4, 1, 1, 1401), type: float64\ndataset created, uuid: d-c2785d13-93b00844-d6c7-228c4b-55a8c6, chunk_size: (4, 1, 1, 1401)\ncreating dataset /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4, shape: (4, 1, 1, 1401), type: float64\ndataset created, uuid: d-c2785d13-93b00844-0a5a-e1d533-274bdc, chunk_size: (4, 1, 1, 1401)\ncreating dataset /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5, shape: (4, 1, 1, 1401), type: float64\ndataset created, uuid: d-c2785d13-93b00844-018a-9a1f1d-d4eeac, chunk_size: (4, 1, 1, 1401)\ncreating dataset /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6, shape: (4, 1, 1, 1401), type: float64\ndataset created, uuid: d-c2785d13-93b00844-5ac4-4bd79f-e1cebe, chunk_size: (4, 1, 1, 1401)\ncreating attribute combineArchiveLocation in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml\ncreating attribute uri in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml\ncreating attribute _type in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1\ncreating attribute sedmlDataSetDataTypes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1\ncreating attribute sedmlDataSetIds in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1\ncreating attribute sedmlDataSetLabels in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1\ncreating attribute sedmlDataSetNames in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1\ncreating attribute sedmlDataSetShapes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1\ncreating attribute sedmlId in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1\ncreating attribute uri in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1\ncreating attribute _type in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2\ncreating attribute sedmlDataSetDataTypes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2\ncreating attribute sedmlDataSetIds in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2\ncreating attribute sedmlDataSetLabels in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2\ncreating attribute sedmlDataSetNames in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2\ncreating attribute sedmlDataSetShapes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2\ncreating attribute sedmlId in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2\ncreating attribute uri in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2\ncreating attribute _type in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3\ncreating attribute sedmlDataSetDataTypes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3\ncreating attribute sedmlDataSetIds in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3\ncreating attribute sedmlDataSetLabels in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3\ncreating attribute sedmlDataSetNames in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3\ncreating attribute sedmlDataSetShapes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3\ncreating attribute sedmlId in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3\ncreating attribute uri in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3\ncreating attribute _type in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4\ncreating attribute sedmlDataSetDataTypes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4\ncreating attribute sedmlDataSetIds in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4\ncreating attribute sedmlDataSetLabels in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4\ncreating attribute sedmlDataSetNames in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4\ncreating attribute sedmlDataSetShapes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4\ncreating attribute sedmlId in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4\ncreating attribute uri in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4\ncreating attribute _type in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5\ncreating attribute sedmlDataSetDataTypes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5\ncreating attribute sedmlDataSetIds in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5\ncreating attribute sedmlDataSetLabels in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5\ncreating attribute sedmlDataSetNames in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5\ncreating attribute sedmlDataSetShapes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5\ncreating attribute sedmlId in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5\ncreating attribute uri in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5\ncreating attribute _type in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6\ncreating attribute sedmlDataSetDataTypes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6\ncreating attribute sedmlDataSetIds in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6\ncreating attribute sedmlDataSetLabels in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6\ncreating attribute sedmlDataSetNames in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6\ncreating attribute sedmlDataSetShapes in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6\ncreating attribute sedmlId in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6\ncreating attribute uri in /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6\ncreate_links: /\ngot link: barberis_klipp_vanoni_alberghina_2007_Fig3.sedml\ncreate_links: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml\ngot link: plot1\ngot link: plot2\ngot link: plot3\ngot link: plot4\ngot link: plot5\ngot link: plot6\nwrite_dataset src: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1 to tgt: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1, shape: (4, 1, 1, 1401), type: float64\niterating over chunks for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 1401, 1))\ndone with dataload for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot1\nwrite_dataset src: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2 to tgt: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2, shape: (4, 1, 1, 1401), type: float64\niterating over chunks for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 1401, 1))\ndone with dataload for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot2\nwrite_dataset src: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3 to tgt: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3, shape: (4, 1, 1, 1401), type: float64\niterating over chunks for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 1401, 1))\ndone with dataload for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot3\nwrite_dataset src: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4 to tgt: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4, shape: (4, 1, 1, 1401), type: float64\niterating over chunks for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 1401, 1))\ndone with dataload for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot4\nwrite_dataset src: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5 to tgt: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5, shape: (4, 1, 1, 1401), type: float64\niterating over chunks for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 1401, 1))\ndone with dataload for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot5\nwrite_dataset src: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6 to tgt: /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6, shape: (4, 1, 1, 1401), type: float64\niterating over chunks for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6\nwriting dataset data for slice: (slice(0, 4, 1), slice(0, 1, 1), slice(0, 1, 1), slice(0, 1401, 1))\ndone with dataload for /barberis_klipp_vanoni_alberghina_2007_Fig3.sedml/plot6\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6261739190c6a195955782fb\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\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 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.\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","duration":3.24794,"sedDocuments":[{"location":"barberis_klipp_vanoni_alberghina_2007_Fig3.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":" Found 2 tasks and 6 outputs:\n Tasks:\n `repeatedTask`\n `task1`\n Outputs:\n `plot1`\n `plot2`\n `plot3`\n `plot4`\n `plot5`\n `plot6`\n Executing task 1: `repeatedTask`\n Executing simulation ... \u001b[34msucceeded\u001b[0m\n Generating 6 outputs ...\n Generating output 1: `plot1` ... \u001b[34msucceeded\u001b[0m\n Generating output 2: `plot2` ... \u001b[34msucceeded\u001b[0m\n Generating output 3: `plot3` ... \u001b[34msucceeded\u001b[0m\n Generating output 4: `plot4` ... \u001b[34msucceeded\u001b[0m\n Generating output 5: `plot5` ... \u001b[34msucceeded\u001b[0m\n Generating output 6: `plot6` ... \u001b[34msucceeded\u001b[0m\n Executing task 2: `task1`\n Executing simulation ... \u001b[34msucceeded\u001b[0m\n Generating 6 outputs ...\n Generating output 1: `plot1` ... Generating output 2: `plot2` ... Generating output 3: `plot3` ... Generating output 4: `plot4` ... Generating output 5: `plot5` ... Generating output 6: `plot6` .../home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: NoOutputsWarning: \u001b[33mTask task1 does not contribute to any outputs.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n\n Executed 2 tasks and 6 outputs:\n Tasks:\n Succeeded: 2\n Skipped: 0\n Failed: 0\n Outputs:\n Succeeded: 6\n Skipped: 0\n Failed: 0\n","duration":2.646734,"tasks":[{"id":"repeatedTask","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `xVariable2_2` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable2_1` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable1_2` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable6_2` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable5_2` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable4_2` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable4_1` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable1_1` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable2_1` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable1_1` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable4_2` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable3_1` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable2_2` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable3_2` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable6_2` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable5_1` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable3_1` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable3_2` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable5_1` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable1_2` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable4_1` may be invalid.\n - XPath could not be validated.\n- Variable `yVariable6_1` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable6_1` may be invalid.\n - XPath could not be validated.\n- Variable `xVariable5_2` may be invalid.\n - XPath could not be validated.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n - The following tasks do not contribute to outputs:\n - `repeatedTask`\n - `task1`\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.772175,"algorithm":null,"simulatorDetails":null},{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\n - The following tasks do not contribute to outputs:\n - `repeatedTask`\n - `task1`\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.467899,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"OpenCOR.SimulationSupport.Simulation.run"},{"key":"algorithmParameters","value":[{"kisaoID":"KISAO_0000211","value":1e-7},{"kisaoID":"KISAO_0000475","value":"BDF"},{"kisaoID":"KISAO_0000481","value":"true"},{"kisaoID":"KISAO_0000476","value":"Newton"},{"kisaoID":"KISAO_0000477","value":"Dense"},{"kisaoID":"KISAO_0000480","value":"0"},{"kisaoID":"KISAO_0000415","value":"500"},{"kisaoID":"KISAO_0000467","value":"0"},{"kisaoID":"KISAO_0000478","value":"Banded"},{"kisaoID":"KISAO_0000209","value":1e-7},{"kisaoID":"KISAO_0000479","value":"0"}]}]}],"outputs":[{"id":"plot1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/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\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.216877,"curves":[{"id":"curve1_1","status":"SUCCEEDED"},{"id":"curve1_2","status":"SUCCEEDED"}]},{"id":"plot2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/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\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.179552,"curves":[{"id":"curve2_1","status":"SUCCEEDED"},{"id":"curve2_2","status":"SUCCEEDED"}]},{"id":"plot3","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/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\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.19093,"curves":[{"id":"curve3_1","status":"SUCCEEDED"},{"id":"curve3_2","status":"SUCCEEDED"}]},{"id":"plot4","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/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\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.188313,"curves":[{"id":"curve4_1","status":"SUCCEEDED"},{"id":"curve4_2","status":"SUCCEEDED"}]},{"id":"plot5","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/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\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.182023,"curves":[{"id":"curve5_1","status":"SUCCEEDED"},{"id":"curve5_2","status":"SUCCEEDED"}]},{"id":"plot6","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"/home/opencor/OpenCOR/python/lib/python3.7/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the X axis because the X data generators have inconsistent names.\u001b[0m\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n/home/opencor/OpenCOR/python/lib/python3.7/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\n warnings.warn(termcolor.colored(message, Colors.warning.value), category)\n","duration":0.186292,"curves":[{"id":"curve6_1","status":"SUCCEEDED"},{"id":"curve6_2","status":"SUCCEEDED"}]}]}]}