{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    406      0 --:--:-- --:--:-- --:--:--   406\n\r100  224k  100  224k    0     0   489k      0 --:--:-- --:--:-- --:--:--  489k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\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 log ====================================================\u001b[0m\nCompleted 1.6 KiB/1.6 KiB (21.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/rawLog.txt\nCompleted 3.9 KiB/3.9 KiB (56.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/BIOMD0000000192_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000192_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 10%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 240.2 KiB/240.2 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/outputs/reports.h5\nCompleted 228.4 KiB/251.8 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/output.zip\nCompleted 228.4 KiB/251.8 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 236.8 KiB/251.8 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/outputs/plots.zip\nCompleted 236.8 KiB/251.8 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 249.1 KiB/251.8 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000192_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/outputs/BIOMD0000000192_url.sedml/autogen_plot_for_task1.pdf\nCompleted 249.1 KiB/251.8 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 251.8 KiB/251.8 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000192-biopax2.owl  \n  inflating: contents/BIOMD0000000192-biopax3.owl  \n  inflating: contents/BIOMD0000000192-matlab.m  \n  inflating: contents/BIOMD0000000192.m  \n  inflating: contents/BIOMD0000000192.ode  \n  inflating: contents/BIOMD0000000192.pdf  \n  inflating: contents/BIOMD0000000192.png  \n  inflating: contents/BIOMD0000000192.svg  \n  inflating: contents/BIOMD0000000192_url.sedml  \n  inflating: contents/BIOMD0000000192_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 23.3 KiB/419.9 KiB (326.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000192-biopax2.owl to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/BIOMD0000000192-biopax2.owl\nCompleted 23.3 KiB/419.9 KiB (326.1 KiB/s) with 13 file(s) remaining\rCompleted 57.8 KiB/419.9 KiB (489.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000192-biopax3.owl to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/BIOMD0000000192-biopax3.owl\nCompleted 57.8 KiB/419.9 KiB (489.7 KiB/s) with 12 file(s) remaining\rCompleted 83.9 KiB/419.9 KiB (675.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000192.svg to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/BIOMD0000000192.svg\nCompleted 83.9 KiB/419.9 KiB (675.5 KiB/s) with 11 file(s) remaining\rCompleted 91.2 KiB/419.9 KiB (723.3 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000192-matlab.m to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/BIOMD0000000192-matlab.m\nCompleted 91.2 KiB/419.9 KiB (723.3 KiB/s) with 10 file(s) remaining\rCompleted 107.6 KiB/419.9 KiB (718.7 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000192_url.sedml to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/BIOMD0000000192_url.sedml\nCompleted 107.6 KiB/419.9 KiB (718.7 KiB/s) with 9 file(s) remaining\rCompleted 116.0 KiB/419.9 KiB (769.5 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/curation_image.png\nCompleted 116.0 KiB/419.9 KiB (769.5 KiB/s) with 8 file(s) remaining\rCompleted 117.6 KiB/419.9 KiB (720.4 KiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/manifest.xml\nCompleted 117.6 KiB/419.9 KiB (720.4 KiB/s) with 7 file(s) remaining\rCompleted 147.3 KiB/419.9 KiB (861.2 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000192_url.xml to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/BIOMD0000000192_url.xml\nCompleted 147.3 KiB/419.9 KiB (861.2 KiB/s) with 6 file(s) remaining\rCompleted 147.5 KiB/419.9 KiB (842.8 KiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/curation_notes.txt\nCompleted 147.5 KiB/419.9 KiB (842.8 KiB/s) with 5 file(s) remaining\rCompleted 149.6 KiB/419.9 KiB (821.7 KiB/s) with 5 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/metadata.rdf\nCompleted 149.6 KiB/419.9 KiB (821.7 KiB/s) with 4 file(s) remaining\rCompleted 154.3 KiB/419.9 KiB (821.7 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000192.ode to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/BIOMD0000000192.ode\nCompleted 154.3 KiB/419.9 KiB (821.7 KiB/s) with 3 file(s) remaining\rCompleted 161.6 KiB/419.9 KiB (788.0 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000192.m to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/BIOMD0000000192.m\nCompleted 161.6 KiB/419.9 KiB (788.0 KiB/s) with 2 file(s) remaining\rCompleted 345.1 KiB/419.9 KiB (1.5 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000192.pdf to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/BIOMD0000000192.pdf\nCompleted 345.1 KiB/419.9 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 419.9 KiB/419.9 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000192.png to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/contents/BIOMD0000000192.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.3 KiB/8.3 KiB (83.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471096b0dcacb55678b7a50/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000192_url.sedml\ncreating dataset /BIOMD0000000192_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\ndataset created, uuid: d-a2f57c67-9152573f-edb2-0199ee-85216e, chunk_size: (14, 1001)\ncreating dataset /BIOMD0000000192_url.sedml/autogen_report_for_task1, shape: (25, 1001), type: float64\ndataset created, uuid: d-a2f57c67-9152573f-f19b-6c2b01-8b9101, chunk_size: (25, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000192_url.sedml\ncreating attribute uri in /BIOMD0000000192_url.sedml\ncreating attribute _type in /BIOMD0000000192_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000192_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000192_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000192_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000192_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000192_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000192_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000192_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000192_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000192_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000192_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000192_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000192_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000192_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000192_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000192_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000192_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000192_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000192_url.sedml\ncreate_links: /BIOMD0000000192_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000192_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000192_url.sedml/autogen_plot_for_task1, shape: (14, 1001), type: float64\niterating over chunks for /BIOMD0000000192_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 14, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000192_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000192_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000192_url.sedml/autogen_report_for_task1, shape: (25, 1001), type: float64\niterating over chunks for /BIOMD0000000192_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 25, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000192_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471096b0dcacb55678b7a50\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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.45566,"sedDocuments":[{"location":"BIOMD0000000192_url.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  BIOMD0000000192_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 25 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 13 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000192_url.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_plot_for_task1`\r\n      `autogen_report_for_task1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `autogen_report_for_task1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_plot_for_task1` ...","duration":1.071787,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.160588,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"deterministic"},{"key":"methodCode","value":22},{"key":"parameters"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.230182,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_RanGDP_nuc","status":"SUCCEEDED"},{"id":"autogen_task1_RCC1_RanGDP","status":"SUCCEEDED"},{"id":"autogen_task1_GDP","status":"SUCCEEDED"},{"id":"autogen_task1_RCC1","status":"SUCCEEDED"},{"id":"autogen_task1_RCC1_RanGTP","status":"SUCCEEDED"},{"id":"autogen_task1_RCC1_Ran","status":"SUCCEEDED"},{"id":"autogen_task1_GTP","status":"SUCCEEDED"},{"id":"autogen_task1_RanGTP_nuc","status":"SUCCEEDED"},{"id":"autogen_task1_RanGAP","status":"SUCCEEDED"},{"id":"autogen_task1_RanBP1","status":"SUCCEEDED"},{"id":"autogen_task1_RanGTP_cy","status":"SUCCEEDED"},{"id":"autogen_task1_RanGTP_RanBP1","status":"SUCCEEDED"},{"id":"autogen_task1_RanGDP_cy","status":"SUCCEEDED"},{"id":"autogen_task1_nucleus","status":"SUCCEEDED"},{"id":"autogen_task1_cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_RCC1_binding","status":"SUCCEEDED"},{"id":"autogen_task1_GDP_dissociation","status":"SUCCEEDED"},{"id":"autogen_task1_GTP_binding","status":"SUCCEEDED"},{"id":"autogen_task1_RanGTP_release","status":"SUCCEEDED"},{"id":"autogen_task1_Cytoplasmic_transfer","status":"SUCCEEDED"},{"id":"autogen_task1_Nucleoplasmic_transfer","status":"SUCCEEDED"},{"id":"autogen_task1_RanGTP_binding","status":"SUCCEEDED"},{"id":"autogen_task1_RanBP1_RanGDP","status":"SUCCEEDED"},{"id":"autogen_task1_RanGAP_RanGDP","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.543988,"curves":[{"id":"autogen_curve_task1_RanGDP_nuc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RCC1_RanGDP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GDP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RCC1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RCC1_RanGTP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RCC1_Ran","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GTP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RanGTP_nuc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RanGAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RanBP1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RanGTP_cy","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RanGTP_RanBP1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RanGDP_cy","status":"SUCCEEDED"}]}]}]}