{"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    432      0 --:--:-- --:--:-- --:--:--   431\n\r100  246k  100  246k    0     0   550k      0 --:--:-- --:--:-- --:--:--  550k\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 (19.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/rawLog.txt\nCompleted 4.4 KiB/4.4 KiB (54.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000187_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000187_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/reports.h5 (deflated 12%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 244.6 KiB/244.6 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/outputs/reports.h5\nCompleted 10.0 KiB/254.9 KiB (95.3 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/outputs/plots.zip\nCompleted 10.0 KiB/254.9 KiB (95.3 KiB/s) with 3 file(s) remaining\rCompleted 238.0 KiB/254.9 KiB (2.1 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/output.zip\nCompleted 238.0 KiB/254.9 KiB (2.1 MiB/s) with 2 file(s) remaining\rCompleted 252.2 KiB/254.9 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000187_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/outputs/BIOMD0000000187_url.sedml/autogen_plot_for_task1.pdf\nCompleted 252.2 KiB/254.9 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 254.9 KiB/254.9 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000187-biopax2.owl  \n  inflating: contents/BIOMD0000000187-biopax3.owl  \n  inflating: contents/BIOMD0000000187-matlab.m  \n  inflating: contents/BIOMD0000000187-octave.m  \n  inflating: contents/BIOMD0000000187.m  \n  inflating: contents/BIOMD0000000187.ode  \n  inflating: contents/BIOMD0000000187.pdf  \n  inflating: contents/BIOMD0000000187.png  \n  inflating: contents/BIOMD0000000187.svg  \n  inflating: contents/BIOMD0000000187.vcml  \n  inflating: contents/BIOMD0000000187_url.sedml  \n  inflating: contents/BIOMD0000000187_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 42.6 KiB/534.7 KiB (557.2 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000187-biopax3.owl to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187-biopax3.owl\nCompleted 42.6 KiB/534.7 KiB (557.2 KiB/s) with 15 file(s) remaining\rCompleted 48.9 KiB/534.7 KiB (399.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000187-matlab.m to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187-matlab.m\nCompleted 48.9 KiB/534.7 KiB (399.1 KiB/s) with 14 file(s) remaining\rCompleted 50.8 KiB/534.7 KiB (379.3 KiB/s) with 14 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/manifest.xml\nCompleted 50.8 KiB/534.7 KiB (379.3 KiB/s) with 13 file(s) remaining\rCompleted 57.1 KiB/534.7 KiB (413.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000187-octave.m to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187-octave.m\nCompleted 57.1 KiB/534.7 KiB (413.7 KiB/s) with 12 file(s) remaining\rCompleted 83.6 KiB/534.7 KiB (587.2 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000187.svg to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187.svg\nCompleted 83.6 KiB/534.7 KiB (587.2 KiB/s) with 11 file(s) remaining\rCompleted 114.0 KiB/534.7 KiB (736.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000187-biopax2.owl to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187-biopax2.owl\nCompleted 114.0 KiB/534.7 KiB (736.8 KiB/s) with 10 file(s) remaining\rCompleted 175.1 KiB/534.7 KiB (1.0 MiB/s) with 10 file(s) remaining  \rupload: contents/BIOMD0000000187.vcml to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187.vcml\nCompleted 175.1 KiB/534.7 KiB (1.0 MiB/s) with 9 file(s) remaining\rCompleted 197.1 KiB/534.7 KiB (1.1 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000187_url.sedml to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187_url.sedml\nCompleted 197.1 KiB/534.7 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 234.2 KiB/534.7 KiB (1.3 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000187_url.xml to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187_url.xml\nCompleted 234.2 KiB/534.7 KiB (1.3 MiB/s) with 7 file(s) remaining\rCompleted 246.8 KiB/534.7 KiB (1.2 MiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/curation_image.png\nCompleted 246.8 KiB/534.7 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 253.1 KiB/534.7 KiB (1.2 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000187.m to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187.m\nCompleted 253.1 KiB/534.7 KiB (1.2 MiB/s) with 5 file(s) remaining\rCompleted 440.7 KiB/534.7 KiB (2.1 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000187.pdf to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187.pdf\nCompleted 440.7 KiB/534.7 KiB (2.1 MiB/s) with 4 file(s) remaining\rCompleted 440.8 KiB/534.7 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/curation_notes.txt\nCompleted 440.8 KiB/534.7 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 449.2 KiB/534.7 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/metadata.rdf\nCompleted 449.2 KiB/534.7 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 530.5 KiB/534.7 KiB (2.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000187.png to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187.png\nCompleted 530.5 KiB/534.7 KiB (2.4 MiB/s) with 1 file(s) remaining\rCompleted 534.7 KiB/534.7 KiB (2.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000187.ode to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/contents/BIOMD0000000187.ode\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (96.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471095b0dcacb55678b7876/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000187_url.sedml\ncreating dataset /BIOMD0000000187_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-96f44808-65cb2df7-1e78-4c0f55-6ded3b, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000187_url.sedml/autogen_report_for_task1, shape: (39, 1001), type: float64\ndataset created, uuid: d-96f44808-65cb2df7-6a20-65982c-c0ffd5, chunk_size: (39, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000187_url.sedml\ncreating attribute uri in /BIOMD0000000187_url.sedml\ncreating attribute _type in /BIOMD0000000187_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000187_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000187_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000187_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000187_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000187_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000187_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000187_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000187_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000187_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000187_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000187_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000187_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000187_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000187_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000187_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000187_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000187_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000187_url.sedml\ncreate_links: /BIOMD0000000187_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000187_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000187_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000187_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000187_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000187_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000187_url.sedml/autogen_report_for_task1, shape: (39, 1001), type: float64\niterating over chunks for /BIOMD0000000187_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 39, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000187_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471095b0dcacb55678b7876\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 the metadata in the COMBINE archive ... succeeded.\nPost the metadata 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.\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":1.965247,"sedDocuments":[{"location":"BIOMD0000000187_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  BIOMD0000000187_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 39 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000187_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":1.290706,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.193503,"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":0.355822,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_Mad1_CMad2","status":"SUCCEEDED"},{"id":"autogen_task1_OMad2","status":"SUCCEEDED"},{"id":"autogen_task1_Mad1_CMad2_OMad2","status":"SUCCEEDED"},{"id":"autogen_task1_Cdc20","status":"SUCCEEDED"},{"id":"autogen_task1_Cdc20_CMad2","status":"SUCCEEDED"},{"id":"autogen_task1_Bub3_BubR1","status":"SUCCEEDED"},{"id":"autogen_task1_MCC","status":"SUCCEEDED"},{"id":"autogen_task1_Bub3_BubR1_Cdc20","status":"SUCCEEDED"},{"id":"autogen_task1_APC","status":"SUCCEEDED"},{"id":"autogen_task1_MCC_APC","status":"SUCCEEDED"},{"id":"autogen_task1_APC_Cdc20","status":"SUCCEEDED"},{"id":"autogen_task1_k3f","status":"SUCCEEDED"},{"id":"autogen_task1_kf6","status":"SUCCEEDED"},{"id":"autogen_task1_k5f","status":"SUCCEEDED"},{"id":"autogen_task1_k5r","status":"SUCCEEDED"},{"id":"autogen_task1_k2f","status":"SUCCEEDED"},{"id":"autogen_task1_k1f","status":"SUCCEEDED"},{"id":"autogen_task1_k1r","status":"SUCCEEDED"},{"id":"autogen_task1_k4f","status":"SUCCEEDED"},{"id":"autogen_task1_k4r","status":"SUCCEEDED"},{"id":"autogen_task1_k7f","status":"SUCCEEDED"},{"id":"autogen_task1_k7bf","status":"SUCCEEDED"},{"id":"autogen_task1_k8f","status":"SUCCEEDED"},{"id":"autogen_task1_k8r","status":"SUCCEEDED"},{"id":"autogen_task1_u","status":"SUCCEEDED"},{"id":"autogen_task1_u_prime","status":"SUCCEEDED"},{"id":"autogen_task1_const_val_0","status":"SUCCEEDED"},{"id":"autogen_task1_const_val_1","status":"SUCCEEDED"},{"id":"autogen_task1_Cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"},{"id":"autogen_task1_R5","status":"SUCCEEDED"},{"id":"autogen_task1_R6","status":"SUCCEEDED"},{"id":"autogen_task1_R7","status":"SUCCEEDED"},{"id":"autogen_task1_R7b","status":"SUCCEEDED"},{"id":"autogen_task1_R8","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.577658,"curves":[{"id":"autogen_curve_task1_Mad1_CMad2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OMad2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mad1_CMad2_OMad2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cdc20","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cdc20_CMad2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Bub3_BubR1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MCC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Bub3_BubR1_Cdc20","status":"SUCCEEDED"},{"id":"autogen_curve_task1_APC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_MCC_APC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_APC_Cdc20","status":"SUCCEEDED"}]}]}]}