{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T_baseline"},{"status":"SUCCEEDED","id":"data_set_EXC2_baseline"},{"status":"SUCCEEDED","id":"data_set_FV1_baseline"},{"status":"SUCCEEDED","id":"data_set_FV2_baseline"},{"status":"SUCCEEDED","id":"data_set_FV3_baseline"},{"status":"SUCCEEDED","id":"data_set_FV4_baseline"},{"status":"SUCCEEDED","id":"data_set_H1_baseline"},{"status":"SUCCEEDED","id":"data_set_H2_baseline"},{"status":"SUCCEEDED","id":"data_set_H3_baseline"},{"status":"SUCCEEDED","id":"data_set_H4_baseline"},{"status":"SUCCEEDED","id":"data_set_INH1_baseline"},{"status":"SUCCEEDED","id":"data_set_INH2_baseline"},{"status":"SUCCEEDED","id":"data_set_INH3_baseline"},{"status":"SUCCEEDED","id":"data_set_INH4_baseline"},{"status":"SUCCEEDED","id":"data_set_M2_baseline"},{"status":"SUCCEEDED","id":"data_set_M3_baseline"},{"status":"SUCCEEDED","id":"data_set_M4_baseline"},{"status":"SUCCEEDED","id":"data_set_V1_baseline"},{"status":"SUCCEEDED","id":"data_set_V2_baseline"},{"status":"SUCCEEDED","id":"data_set_V3_baseline"},{"status":"SUCCEEDED","id":"data_set_V4_baseline"}],"duration":0.167471,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report_baseline"},{"curves":[{"status":"SUCCEEDED","id":"curve_1_baseline"}],"duration":0.166307,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot_baseline"}],"tasks":[{"simulatorDetails":[{"value":"10000.0","key":"total"},{"value":"qualrk","key":"meth"},{"value":1e-12,"key":"dtmin"},{"value":"1","key":"dtmax"},{"value":"0.001","key":"toler"},{"value":"0.001","key":"newt_tol"},{"value":"0.0","key":"t0"},{"value":"10","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000672","duration":0.207322,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task_baseline"}],"duration":0.708957,"output":"Archive contains 3 SED-ML documents with 6 models, 3 simulations, 3 tasks, 3 reports, and 2 plots:\r\n  basenet.sedml:\r\n    Tasks (1):\r\n      task_baseline\r\n    Reports (1):\r\n      report_baseline: 21 data sets\r\n    Plots (1):\r\n      plot_baseline: 1 curves\r\n  basenetTA.sedml:\r\n    Tasks (1):\r\n      task_with_pico\r\n    Reports (1):\r\n      report_with_pico: 21 data sets\r\n  basenetpico3.sedml:\r\n    Tasks (1):\r\n      task_without_pico_block_of_inhibition\r\n    Reports (1):\r\n      report_without_pico_block_of_inhibition: 24 data sets\r\n    Plots (1):\r\n      plot_without_pico_block_of_inhibition: 1 curves\r\n\r\nExecuting SED-ML file 1: basenet.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task_baseline`\r\n    Outputs:\r\n      `plot_baseline`\r\n      `report_baseline`\r\n  Executing task 1: `task_baseline`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `report_baseline` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_baseline` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"basenet.sedml"},{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T_with_pico"},{"status":"SUCCEEDED","id":"data_set_EXC2_with_pico"},{"status":"SUCCEEDED","id":"data_set_FV1_with_pico"},{"status":"SUCCEEDED","id":"data_set_FV2_with_pico"},{"status":"SUCCEEDED","id":"data_set_FV3_with_pico"},{"status":"SUCCEEDED","id":"data_set_FV4_with_pico"},{"status":"SUCCEEDED","id":"data_set_H1_with_pico"},{"status":"SUCCEEDED","id":"data_set_H2_with_pico"},{"status":"SUCCEEDED","id":"data_set_H3_with_pico"},{"status":"SUCCEEDED","id":"data_set_H4_with_pico"},{"status":"SUCCEEDED","id":"data_set_INH1_with_pico"},{"status":"SUCCEEDED","id":"data_set_INH2_with_pico"},{"status":"SUCCEEDED","id":"data_set_INH3_with_pico"},{"status":"SUCCEEDED","id":"data_set_INH4_with_pico"},{"status":"SUCCEEDED","id":"data_set_M2_with_pico"},{"status":"SUCCEEDED","id":"data_set_M3_with_pico"},{"status":"SUCCEEDED","id":"data_set_M4_with_pico"},{"status":"SUCCEEDED","id":"data_set_V1_with_pico"},{"status":"SUCCEEDED","id":"data_set_V2_with_pico"},{"status":"SUCCEEDED","id":"data_set_V3_with_pico"},{"status":"SUCCEEDED","id":"data_set_V4_with_pico"}],"duration":0.158138,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report_with_pico"}],"tasks":[{"simulatorDetails":[{"value":"25000.0","key":"total"},{"value":"10000.0","key":"trans"},{"value":"qualrk","key":"meth"},{"value":1e-12,"key":"dtmin"},{"value":"1","key":"dtmax"},{"value":"0.00001","key":"toler"},{"value":"0.001","key":"newt_tol"},{"value":"0.0","key":"t0"},{"value":"5","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000672","duration":0.339309,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task_with_pico"}],"duration":0.634124,"output":" \u001b[34msucceeded\u001b[0m\r\n\r\n  Executed 1 tasks and 2 outputs:\r\n    Tasks:\r\n      Succeeded: 1\r\n      Skipped: 0\r\n      Failed: 0\r\n    Outputs:\r\n      Succeeded: 2\r\n      Skipped: 0\r\n      Failed: 0\r\nExecuting SED-ML file 2: basenetTA.sedml ...\r\n  Found 1 tasks and 1 outputs:\r\n    Tasks:\r\n      `task_with_pico`\r\n    Outputs:\r\n      `report_with_pico`\r\n  Executing task 1: `task_with_pico`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 1 outputs ...\r\n      Generating output 1: `report_with_pico` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"basenetTA.sedml"},{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_EXC2_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_FV1_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_FV2_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_FV3_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_FV4_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_FV5_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_H1_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_H2_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_H3_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_H4_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_H5_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_INH1_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_INH2_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_INH3_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_INH4_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_M2_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_M3_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_M4_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_V1_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_V2_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_V3_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_V4_without_pico_block_of_inhibition"},{"status":"SUCCEEDED","id":"data_set_V5_without_pico_block_of_inhibition"}],"duration":0.175513,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report_without_pico_block_of_inhibition"},{"curves":[{"status":"SUCCEEDED","id":"curve_1_without_pico_block_of_inhibition"}],"duration":0.139138,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot_without_pico_block_of_inhibition"}],"tasks":[{"simulatorDetails":[{"value":"10000.0","key":"total"},{"value":"qualrk","key":"meth"},{"value":1e-12,"key":"dtmin"},{"value":"1","key":"dtmax"},{"value":"0.001","key":"toler"},{"value":"0.001","key":"newt_tol"},{"value":"0.0","key":"t0"},{"value":"10","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000672","duration":0.216353,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task_without_pico_block_of_inhibition"}],"duration":0.7068,"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: basenetpico3.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task_without_pico_block_of_inhibition`\r\n    Outputs:\r\n      `plot_without_pico_block_of_inhibition`\r\n      `report_without_pico_block_of_inhibition`\r\n  Executing task 1: `task_without_pico_block_of_inhibition`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `report_without_pico_block_of_inhibition` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `plot_without_pico_block_of_inhibition` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"basenetpico3.sedml"}],"duration":2.698257,"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    465      0 --:--:-- --:--:-- --:--:--   466\n\r100  910k  100  910k    0     0  2100k      0 --:--:-- --:--:-- --:--:-- 2100k\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 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 (5):\n    Succeeded: 5\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.txt     \n  inflating: contents/basenetTA.ode  \n  inflating: contents/basenetpico3.ode.set3  \n  inflating: contents/basenet.ode    \n  inflating: contents/basenetpico3.ode  \n  inflating: contents/basenetTA.ode.set  \n  inflating: contents/basenet.ode.set  \n  inflating: contents/basenet.sedml  \n  inflating: contents/basenetTA.sedml  \n  inflating: contents/basenetpico3.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g001.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g002.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g003.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g004.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g005.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g006.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g007.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g008.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g009.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g010.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g011.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g012.jpg  \n  inflating: contents/article-figures/PMC6697358/pcbi.1006860.g013.jpg  \n  inflating: contents/manifest.xml   \nCompleted 113.6 KiB/1.2 MiB (870.6 KiB/s) with 25 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g004.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g004.jpg\nCompleted 113.6 KiB/1.2 MiB (870.6 KiB/s) with 24 file(s) remaining\rCompleted 209.6 KiB/1.2 MiB (1.5 MiB/s) with 24 file(s) remaining  \rupload: contents/article-figures/PMC6697358/pcbi.1006860.g010.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g010.jpg\nCompleted 209.6 KiB/1.2 MiB (1.5 MiB/s) with 23 file(s) remaining\rCompleted 285.2 KiB/1.2 MiB (1.9 MiB/s) with 23 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g011.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g011.jpg\nCompleted 285.2 KiB/1.2 MiB (1.9 MiB/s) with 22 file(s) remaining\rCompleted 354.8 KiB/1.2 MiB (2.3 MiB/s) with 22 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g003.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g003.jpg\nCompleted 354.8 KiB/1.2 MiB (2.3 MiB/s) with 21 file(s) remaining\rCompleted 401.6 KiB/1.2 MiB (2.5 MiB/s) with 21 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g008.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g008.jpg\nCompleted 401.6 KiB/1.2 MiB (2.5 MiB/s) with 20 file(s) remaining\rCompleted 493.0 KiB/1.2 MiB (3.0 MiB/s) with 20 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g012.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g012.jpg\nCompleted 493.0 KiB/1.2 MiB (3.0 MiB/s) with 19 file(s) remaining\rCompleted 570.5 KiB/1.2 MiB (3.4 MiB/s) with 19 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g001.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g001.jpg\nCompleted 570.5 KiB/1.2 MiB (3.4 MiB/s) with 18 file(s) remaining\rCompleted 662.7 KiB/1.2 MiB (3.7 MiB/s) with 18 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g013.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g013.jpg\nCompleted 662.7 KiB/1.2 MiB (3.7 MiB/s) with 17 file(s) remaining\rCompleted 665.4 KiB/1.2 MiB (3.7 MiB/s) with 17 file(s) remaining\rCompleted 780.0 KiB/1.2 MiB (4.3 MiB/s) with 17 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g009.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g009.jpg\nCompleted 780.0 KiB/1.2 MiB (4.3 MiB/s) with 16 file(s) remaining\rCompleted 785.0 KiB/1.2 MiB (4.2 MiB/s) with 16 file(s) remaining\rupload: contents/basenet.ode.set to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/basenet.ode.set\nCompleted 785.0 KiB/1.2 MiB (4.2 MiB/s) with 15 file(s) remaining\rupload: contents/basenet.ode to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/basenet.ode\nCompleted 785.0 KiB/1.2 MiB (4.2 MiB/s) with 14 file(s) remaining\rCompleted 800.1 KiB/1.2 MiB (3.7 MiB/s) with 14 file(s) remaining\rupload: contents/basenet.sedml to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/basenet.sedml\nCompleted 800.1 KiB/1.2 MiB (3.7 MiB/s) with 13 file(s) remaining\rCompleted 803.1 KiB/1.2 MiB (3.7 MiB/s) with 13 file(s) remaining\rupload: contents/basenetTA.ode to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/basenetTA.ode\nCompleted 803.1 KiB/1.2 MiB (3.7 MiB/s) with 12 file(s) remaining\rCompleted 818.3 KiB/1.2 MiB (3.7 MiB/s) with 12 file(s) remaining\rupload: contents/basenetTA.sedml to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/basenetTA.sedml\nCompleted 818.3 KiB/1.2 MiB (3.7 MiB/s) with 11 file(s) remaining\rCompleted 823.7 KiB/1.2 MiB (3.6 MiB/s) with 11 file(s) remaining\rupload: contents/basenetpico3.ode.set3 to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/basenetpico3.ode.set3\nCompleted 823.7 KiB/1.2 MiB (3.6 MiB/s) with 10 file(s) remaining\rCompleted 840.4 KiB/1.2 MiB (3.6 MiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/metadata.rdf\nCompleted 840.4 KiB/1.2 MiB (3.6 MiB/s) with 9 file(s) remaining\rCompleted 842.1 KiB/1.2 MiB (3.6 MiB/s) with 9 file(s) remaining\rupload: contents/readme.txt to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/readme.txt\nCompleted 842.1 KiB/1.2 MiB (3.6 MiB/s) with 8 file(s) remaining\rCompleted 863.0 KiB/1.2 MiB (3.4 MiB/s) with 8 file(s) remaining\rupload: contents/basenetpico3.sedml to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/basenetpico3.sedml\nCompleted 863.0 KiB/1.2 MiB (3.4 MiB/s) with 7 file(s) remaining\rCompleted 866.3 KiB/1.2 MiB (3.3 MiB/s) with 7 file(s) remaining\rupload: contents/basenetpico3.ode to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/basenetpico3.ode\nCompleted 866.3 KiB/1.2 MiB (3.3 MiB/s) with 6 file(s) remaining\rCompleted 999.3 KiB/1.2 MiB (3.5 MiB/s) with 6 file(s) remaining\rCompleted 1002.4 KiB/1.2 MiB (3.5 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/manifest.xml\nCompleted 1002.4 KiB/1.2 MiB (3.5 MiB/s) with 5 file(s) remaining\rCompleted 1.0 MiB/1.2 MiB (3.7 MiB/s) with 5 file(s) remaining   \rupload: contents/article-figures/PMC6697358/pcbi.1006860.g002.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g002.jpg\nCompleted 1.0 MiB/1.2 MiB (3.7 MiB/s) with 4 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g005.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g005.jpg\nCompleted 1.0 MiB/1.2 MiB (3.7 MiB/s) with 3 file(s) remaining\rCompleted 1.1 MiB/1.2 MiB (3.8 MiB/s) with 3 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g007.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g007.jpg\nCompleted 1.1 MiB/1.2 MiB (3.8 MiB/s) with 2 file(s) remaining\rCompleted 1.1 MiB/1.2 MiB (3.6 MiB/s) with 2 file(s) remaining\rupload: contents/basenetTA.ode.set to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/basenetTA.ode.set\nCompleted 1.1 MiB/1.2 MiB (3.6 MiB/s) with 1 file(s) remaining\rCompleted 1.2 MiB/1.2 MiB (3.8 MiB/s) with 1 file(s) remaining\rupload: contents/article-figures/PMC6697358/pcbi.1006860.g006.jpg to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/contents/article-figures/PMC6697358/pcbi.1006860.g006.jpg\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /basenet.sedml\ncreating dataset /basenet.sedml/plot_baseline, shape: (2, 1001), type: float64\ndataset created, uuid: d-bac74d63-b2bf1f06-39e4-3e95c1-ec4c07, chunk_size: (2, 1001)\ncreating dataset /basenet.sedml/report_baseline, shape: (21, 1001), type: float64\ndataset created, uuid: d-bac74d63-b2bf1f06-97f6-a6b206-67f25b, chunk_size: (21, 1001)\ncreating group /basenetTA.sedml\ncreating dataset /basenetTA.sedml/report_with_pico, shape: (21, 1001), type: float64\ndataset created, uuid: d-bac74d63-b2bf1f06-45fd-369bbe-9a516f, chunk_size: (21, 1001)\ncreating group /basenetpico3.sedml\ncreating dataset /basenetpico3.sedml/plot_without_pico_block_of_inhibition, shape: (2, 1001), type: float64\ndataset created, uuid: d-bac74d63-b2bf1f06-13fe-4cf216-d8150d, chunk_size: (2, 1001)\ncreating dataset /basenetpico3.sedml/report_without_pico_block_of_inhibition, shape: (24, 1001), type: float64\ndataset created, uuid: d-bac74d63-b2bf1f06-373f-e0bac6-1462ba, chunk_size: (24, 1001)\ncreating attribute combineArchiveLocation in /basenet.sedml\ncreating attribute uri in /basenet.sedml\ncreating attribute _type in /basenet.sedml/plot_baseline\ncreating attribute sedmlDataSetDataTypes in /basenet.sedml/plot_baseline\ncreating attribute sedmlDataSetIds in /basenet.sedml/plot_baseline\ncreating attribute sedmlDataSetLabels in /basenet.sedml/plot_baseline\ncreating attribute sedmlDataSetNames in /basenet.sedml/plot_baseline\ncreating attribute sedmlDataSetShapes in /basenet.sedml/plot_baseline\ncreating attribute sedmlId in /basenet.sedml/plot_baseline\ncreating attribute sedmlName in /basenet.sedml/plot_baseline\ncreating attribute uri in /basenet.sedml/plot_baseline\ncreating attribute _type in /basenet.sedml/report_baseline\ncreating attribute sedmlDataSetDataTypes in /basenet.sedml/report_baseline\ncreating attribute sedmlDataSetIds in /basenet.sedml/report_baseline\ncreating attribute sedmlDataSetLabels in /basenet.sedml/report_baseline\ncreating attribute sedmlDataSetNames in /basenet.sedml/report_baseline\ncreating attribute sedmlDataSetShapes in /basenet.sedml/report_baseline\ncreating attribute sedmlId in /basenet.sedml/report_baseline\ncreating attribute sedmlName in /basenet.sedml/report_baseline\ncreating attribute uri in /basenet.sedml/report_baseline\ncreating attribute combineArchiveLocation in /basenetTA.sedml\ncreating attribute uri in /basenetTA.sedml\ncreating attribute _type in /basenetTA.sedml/report_with_pico\ncreating attribute sedmlDataSetDataTypes in /basenetTA.sedml/report_with_pico\ncreating attribute sedmlDataSetIds in /basenetTA.sedml/report_with_pico\ncreating attribute sedmlDataSetLabels in /basenetTA.sedml/report_with_pico\ncreating attribute sedmlDataSetNames in /basenetTA.sedml/report_with_pico\ncreating attribute sedmlDataSetShapes in /basenetTA.sedml/report_with_pico\ncreating attribute sedmlId in /basenetTA.sedml/report_with_pico\ncreating attribute sedmlName in /basenetTA.sedml/report_with_pico\ncreating attribute uri in /basenetTA.sedml/report_with_pico\ncreating attribute combineArchiveLocation in /basenetpico3.sedml\ncreating attribute uri in /basenetpico3.sedml\ncreating attribute _type in /basenetpico3.sedml/plot_without_pico_block_of_inhibition\ncreating attribute sedmlDataSetDataTypes in /basenetpico3.sedml/plot_without_pico_block_of_inhibition\ncreating attribute sedmlDataSetIds in /basenetpico3.sedml/plot_without_pico_block_of_inhibition\ncreating attribute sedmlDataSetLabels in /basenetpico3.sedml/plot_without_pico_block_of_inhibition\ncreating attribute sedmlDataSetNames in /basenetpico3.sedml/plot_without_pico_block_of_inhibition\ncreating attribute sedmlDataSetShapes in /basenetpico3.sedml/plot_without_pico_block_of_inhibition\ncreating attribute sedmlId in /basenetpico3.sedml/plot_without_pico_block_of_inhibition\ncreating attribute sedmlName in /basenetpico3.sedml/plot_without_pico_block_of_inhibition\ncreating attribute uri in /basenetpico3.sedml/plot_without_pico_block_of_inhibition\ncreating attribute _type in /basenetpico3.sedml/report_without_pico_block_of_inhibition\ncreating attribute sedmlDataSetDataTypes in /basenetpico3.sedml/report_without_pico_block_of_inhibition\ncreating attribute sedmlDataSetIds in /basenetpico3.sedml/report_without_pico_block_of_inhibition\ncreating attribute sedmlDataSetLabels in /basenetpico3.sedml/report_without_pico_block_of_inhibition\ncreating attribute sedmlDataSetNames in /basenetpico3.sedml/report_without_pico_block_of_inhibition\ncreating attribute sedmlDataSetShapes in /basenetpico3.sedml/report_without_pico_block_of_inhibition\ncreating attribute sedmlId in /basenetpico3.sedml/report_without_pico_block_of_inhibition\ncreating attribute sedmlName in /basenetpico3.sedml/report_without_pico_block_of_inhibition\ncreating attribute uri in /basenetpico3.sedml/report_without_pico_block_of_inhibition\ncreate_links: /\ngot link: basenet.sedml\ngot link: basenetTA.sedml\ngot link: basenetpico3.sedml\ncreate_links: /basenet.sedml\ngot link: plot_baseline\ngot link: report_baseline\ncreate_links: /basenetTA.sedml\ngot link: report_with_pico\ncreate_links: /basenetpico3.sedml\ngot link: plot_without_pico_block_of_inhibition\ngot link: report_without_pico_block_of_inhibition\nwrite_dataset src: /basenet.sedml/plot_baseline to tgt: /basenet.sedml/plot_baseline, shape: (2, 1001), type: float64\niterating over chunks for /basenet.sedml/plot_baseline\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /basenet.sedml/plot_baseline\nwrite_dataset src: /basenet.sedml/report_baseline to tgt: /basenet.sedml/report_baseline, shape: (21, 1001), type: float64\niterating over chunks for /basenet.sedml/report_baseline\nwriting dataset data for slice: (slice(0, 21, 1), slice(0, 1001, 1))\ndone with dataload for /basenet.sedml/report_baseline\nwrite_dataset src: /basenetTA.sedml/report_with_pico to tgt: /basenetTA.sedml/report_with_pico, shape: (21, 1001), type: float64\niterating over chunks for /basenetTA.sedml/report_with_pico\nwriting dataset data for slice: (slice(0, 21, 1), slice(0, 1001, 1))\ndone with dataload for /basenetTA.sedml/report_with_pico\nwrite_dataset src: /basenetpico3.sedml/plot_without_pico_block_of_inhibition to tgt: /basenetpico3.sedml/plot_without_pico_block_of_inhibition, shape: (2, 1001), type: float64\niterating over chunks for /basenetpico3.sedml/plot_without_pico_block_of_inhibition\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /basenetpico3.sedml/plot_without_pico_block_of_inhibition\nwrite_dataset src: /basenetpico3.sedml/report_without_pico_block_of_inhibition to tgt: /basenetpico3.sedml/report_without_pico_block_of_inhibition, shape: (24, 1001), type: float64\niterating over chunks for /basenetpico3.sedml/report_without_pico_block_of_inhibition\nwriting dataset data for slice: (slice(0, 24, 1), slice(0, 1001, 1))\ndone with dataload for /basenetpico3.sedml/report_without_pico_block_of_inhibition\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42c4d8a14a834cbf3f8f\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 86%)\n  adding: outputs/basenetpico3.sedml/ (stored 0%)\n  adding: outputs/basenetpico3.sedml/plot_without_pico_block_of_inhibition.pdf (deflated 30%)\n  adding: outputs/basenet.sedml/ (stored 0%)\n  adding: outputs/basenet.sedml/plot_baseline.pdf (deflated 29%)\n  adding: outputs/reports.h5 (deflated 9%)\n  adding: rawLog.txt (deflated 87%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/551.1 KiB (6.1 MiB/s) with 5 file(s) remaining\rCompleted 264.2 KiB/551.1 KiB (3.0 MiB/s) with 5 file(s) remaining\rupload: outputs/basenet.sedml/plot_baseline.pdf to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/outputs/basenet.sedml/plot_baseline.pdf\nCompleted 264.2 KiB/551.1 KiB (3.0 MiB/s) with 4 file(s) remaining\rCompleted 272.2 KiB/551.1 KiB (2.9 MiB/s) with 4 file(s) remaining\rupload: outputs/basenetpico3.sedml/plot_without_pico_block_of_inhibition.pdf to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/outputs/basenetpico3.sedml/plot_without_pico_block_of_inhibition.pdf\nCompleted 272.2 KiB/551.1 KiB (2.9 MiB/s) with 3 file(s) remaining\rCompleted 522.0 KiB/551.1 KiB (5.3 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/output.zip\nCompleted 522.0 KiB/551.1 KiB (5.3 MiB/s) with 2 file(s) remaining\rCompleted 533.2 KiB/551.1 KiB (5.3 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/outputs/plots.zip\nCompleted 533.2 KiB/551.1 KiB (5.3 MiB/s) with 1 file(s) remaining\rCompleted 551.1 KiB/551.1 KiB (4.7 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/rawLog.txt\nCompleted 256.0 KiB/539.3 KiB (6.8 MiB/s) with 1 file(s) remaining\rCompleted 512.0 KiB/539.3 KiB (13.0 MiB/s) with 1 file(s) remaining\rCompleted 539.3 KiB/539.3 KiB (2.4 MiB/s) with 1 file(s) remaining \rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/outputs/reports.h5\nCompleted 10.0 KiB/10.0 KiB (191.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42c4d8a14a834cbf3f8f/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess 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 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 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"}