{"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    407      0 --:--:-- --:--:-- --:--:--   407\n\r100  230k  100  230k    0     0   491k      0 --:--:-- --:--:-- --:--:--  491k\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 (26.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/rawLog.txt\nCompleted 3.7 KiB/3.7 KiB (42.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/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/BIOMD0000000290_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000290_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 184.2 KiB/184.2 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/outputs/reports.h5\nCompleted 164.1 KiB/181.5 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/output.zip\nCompleted 164.1 KiB/181.5 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 169.9 KiB/181.5 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/outputs/plots.zip\nCompleted 169.9 KiB/181.5 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 178.8 KiB/181.5 KiB (1.5 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000290_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/outputs/BIOMD0000000290_url.sedml/autogen_plot_for_task1.pdf\nCompleted 178.8 KiB/181.5 KiB (1.5 MiB/s) with 1 file(s) remaining\rCompleted 181.5 KiB/181.5 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000290-biopax2.owl  \n  inflating: contents/BIOMD0000000290-biopax3.owl  \n  inflating: contents/BIOMD0000000290-matlab.m  \n  inflating: contents/BIOMD0000000290-octave.m  \n  inflating: contents/BIOMD0000000290.m  \n  inflating: contents/BIOMD0000000290.ode  \n  inflating: contents/BIOMD0000000290.pdf  \n  inflating: contents/BIOMD0000000290.png  \n  inflating: contents/BIOMD0000000290.svg  \n  inflating: contents/BIOMD0000000290.vcml  \n  inflating: contents/BIOMD0000000290_url.sedml  \n  inflating: contents/BIOMD0000000290_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 18.0 KiB/406.3 KiB (244.3 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000290-biopax3.owl to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290-biopax3.owl\nCompleted 18.0 KiB/406.3 KiB (244.3 KiB/s) with 15 file(s) remaining\rCompleted 23.2 KiB/406.3 KiB (222.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000290-matlab.m to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290-matlab.m\nCompleted 23.2 KiB/406.3 KiB (222.1 KiB/s) with 14 file(s) remaining\rCompleted 35.3 KiB/406.3 KiB (284.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000290-biopax2.owl to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290-biopax2.owl\nCompleted 35.3 KiB/406.3 KiB (284.0 KiB/s) with 13 file(s) remaining\rCompleted 40.5 KiB/406.3 KiB (312.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000290-octave.m to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290-octave.m\nCompleted 40.5 KiB/406.3 KiB (312.5 KiB/s) with 12 file(s) remaining\rCompleted 42.3 KiB/406.3 KiB (315.1 KiB/s) with 12 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/manifest.xml\nCompleted 42.3 KiB/406.3 KiB (315.1 KiB/s) with 11 file(s) remaining\rCompleted 70.4 KiB/406.3 KiB (488.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000290.vcml to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290.vcml\nCompleted 70.4 KiB/406.3 KiB (488.0 KiB/s) with 10 file(s) remaining\rCompleted 88.8 KiB/406.3 KiB (605.4 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000290_url.sedml to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290_url.sedml\nCompleted 88.8 KiB/406.3 KiB (605.4 KiB/s) with 9 file(s) remaining\rCompleted 110.2 KiB/406.3 KiB (690.4 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000290.svg to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290.svg\nCompleted 110.2 KiB/406.3 KiB (690.4 KiB/s) with 8 file(s) remaining\rCompleted 114.4 KiB/406.3 KiB (700.9 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/metadata.rdf\nCompleted 114.4 KiB/406.3 KiB (700.9 KiB/s) with 7 file(s) remaining\rCompleted 148.1 KiB/406.3 KiB (858.1 KiB/s) with 7 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/curation_image.png\nCompleted 148.1 KiB/406.3 KiB (858.1 KiB/s) with 6 file(s) remaining\rCompleted 168.9 KiB/406.3 KiB (943.2 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000290_url.xml to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290_url.xml\nCompleted 168.9 KiB/406.3 KiB (943.2 KiB/s) with 5 file(s) remaining\rCompleted 174.0 KiB/406.3 KiB (881.5 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000290.m to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290.m\nCompleted 174.0 KiB/406.3 KiB (881.5 KiB/s) with 4 file(s) remaining\rCompleted 350.6 KiB/406.3 KiB (1.7 MiB/s) with 4 file(s) remaining  \rupload: contents/BIOMD0000000290.pdf to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290.pdf\nCompleted 350.6 KiB/406.3 KiB (1.7 MiB/s) with 3 file(s) remaining\rCompleted 353.8 KiB/406.3 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000290.ode to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290.ode\nCompleted 353.8 KiB/406.3 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 406.1 KiB/406.3 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000290.png to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/BIOMD0000000290.png\nCompleted 406.1 KiB/406.3 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 406.3 KiB/406.3 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/contents/curation_notes.txt\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (142.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710ac149c0d898ffddfe7e/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000290_url.sedml\ncreating dataset /BIOMD0000000290_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-5f4de1cb-c8002d85-6873-650ab1-b65a2e, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000290_url.sedml/autogen_report_for_task1, shape: (35, 1001), type: float64\ndataset created, uuid: d-5f4de1cb-c8002d85-e300-d11491-e46e2b, chunk_size: (35, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000290_url.sedml\ncreating attribute uri in /BIOMD0000000290_url.sedml\ncreating attribute _type in /BIOMD0000000290_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000290_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000290_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000290_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000290_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000290_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000290_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000290_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000290_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000290_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000290_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000290_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000290_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000290_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000290_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000290_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000290_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000290_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000290_url.sedml\ncreate_links: /BIOMD0000000290_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000290_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000290_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000290_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000290_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000290_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000290_url.sedml/autogen_report_for_task1, shape: (35, 1001), type: float64\niterating over chunks for /BIOMD0000000290_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 35, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000290_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710ac149c0d898ffddfe7e\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":1.375283,"sedDocuments":[{"location":"BIOMD0000000290_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  BIOMD0000000290_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 35 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000290_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":0.947217,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.142332,"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":0.266559,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_E","status":"SUCCEEDED"},{"id":"autogen_task1_G","status":"SUCCEEDED"},{"id":"autogen_task1_A_im","status":"SUCCEEDED"},{"id":"autogen_task1_v_max","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_pi1","status":"SUCCEEDED"},{"id":"autogen_task1_lambdaE","status":"SUCCEEDED"},{"id":"autogen_task1_muA","status":"SUCCEEDED"},{"id":"autogen_task1_muR","status":"SUCCEEDED"},{"id":"autogen_task1_muE","status":"SUCCEEDED"},{"id":"autogen_task1_muG","status":"SUCCEEDED"},{"id":"autogen_task1_b1","status":"SUCCEEDED"},{"id":"autogen_task1_sigma1","status":"SUCCEEDED"},{"id":"autogen_task1_mA","status":"SUCCEEDED"},{"id":"autogen_task1_mG","status":"SUCCEEDED"},{"id":"autogen_task1_R0","status":"SUCCEEDED"},{"id":"autogen_task1_body","status":"SUCCEEDED"},{"id":"autogen_task1_r1a","status":"SUCCEEDED"},{"id":"autogen_task1_r1b","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_r8","status":"SUCCEEDED"},{"id":"autogen_task1_r9","status":"SUCCEEDED"},{"id":"autogen_task1_r10","status":"SUCCEEDED"},{"id":"autogen_task1_r11","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.410707,"curves":[{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R","status":"SUCCEEDED"},{"id":"autogen_curve_task1_E","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A_im","status":"SUCCEEDED"}]}]}]}