{"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    336      0 --:--:-- --:--:-- --:--:--   335\n\r100  241k  100  241k    0     0   458k      0 --:--:-- --:--:-- --:--:--  458k\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 (23.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/rawLog.txt\nCompleted 3.6 KiB/3.6 KiB (60.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/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/BIOMD0000000615_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000615_url.sedml/autogen_plot_for_task1.pdf (deflated 33%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 185.3 KiB/185.3 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/outputs/reports.h5\nCompleted 165.9 KiB/184.3 KiB (1.8 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/output.zip\nCompleted 165.9 KiB/184.3 KiB (1.8 MiB/s) with 3 file(s) remaining\rCompleted 172.1 KiB/184.3 KiB (1.6 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/outputs/plots.zip\nCompleted 172.1 KiB/184.3 KiB (1.6 MiB/s) with 2 file(s) remaining\rCompleted 181.6 KiB/184.3 KiB (1.6 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000615_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/outputs/BIOMD0000000615_url.sedml/autogen_plot_for_task1.pdf\nCompleted 181.6 KiB/184.3 KiB (1.6 MiB/s) with 1 file(s) remaining\rCompleted 184.3 KiB/184.3 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000615-biopax2.owl  \n  inflating: contents/BIOMD0000000615-biopax3.owl  \n  inflating: contents/BIOMD0000000615-matlab.m  \n  inflating: contents/BIOMD0000000615-octave.m  \n  inflating: contents/BIOMD0000000615.m  \n  inflating: contents/BIOMD0000000615.ode  \n  inflating: contents/BIOMD0000000615.pdf  \n  inflating: contents/BIOMD0000000615.png  \n  inflating: contents/BIOMD0000000615.sci  \n  inflating: contents/BIOMD0000000615.svg  \n  inflating: contents/BIOMD0000000615_url.sedml  \n  inflating: contents/BIOMD0000000615_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 21.0 KiB/467.1 KiB (295.9 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000615-biopax3.owl to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615-biopax3.owl\nCompleted 21.0 KiB/467.1 KiB (295.9 KiB/s) with 15 file(s) remaining\rCompleted 29.2 KiB/467.1 KiB (290.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000615-matlab.m to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615-matlab.m\nCompleted 29.2 KiB/467.1 KiB (290.7 KiB/s) with 14 file(s) remaining\rCompleted 37.4 KiB/467.1 KiB (299.0 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000615-octave.m to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615-octave.m\nCompleted 37.4 KiB/467.1 KiB (299.0 KiB/s) with 13 file(s) remaining\rCompleted 37.7 KiB/467.1 KiB (291.5 KiB/s) with 13 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/curation_notes.txt\nCompleted 37.7 KiB/467.1 KiB (291.5 KiB/s) with 12 file(s) remaining\rCompleted 38.1 KiB/467.1 KiB (291.4 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000615.sci to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615.sci\nCompleted 38.1 KiB/467.1 KiB (291.4 KiB/s) with 11 file(s) remaining\rCompleted 51.8 KiB/467.1 KiB (387.1 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000615-biopax2.owl to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615-biopax2.owl\nCompleted 51.8 KiB/467.1 KiB (387.1 KiB/s) with 10 file(s) remaining\rCompleted 56.4 KiB/467.1 KiB (364.8 KiB/s) with 10 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/metadata.rdf\nCompleted 56.4 KiB/467.1 KiB (364.8 KiB/s) with 9 file(s) remaining\rCompleted 84.4 KiB/467.1 KiB (526.4 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000615.svg to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615.svg\nCompleted 84.4 KiB/467.1 KiB (526.4 KiB/s) with 8 file(s) remaining\rCompleted 102.7 KiB/467.1 KiB (634.3 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000615_url.sedml to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615_url.sedml\nCompleted 102.7 KiB/467.1 KiB (634.3 KiB/s) with 7 file(s) remaining\rCompleted 108.7 KiB/467.1 KiB (563.9 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000615.ode to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615.ode\nCompleted 108.7 KiB/467.1 KiB (563.9 KiB/s) with 6 file(s) remaining\rCompleted 121.7 KiB/467.1 KiB (627.8 KiB/s) with 6 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/curation_image.png\nCompleted 121.7 KiB/467.1 KiB (627.8 KiB/s) with 5 file(s) remaining\rCompleted 130.0 KiB/467.1 KiB (657.8 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000615.m to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615.m\nCompleted 130.0 KiB/467.1 KiB (657.8 KiB/s) with 4 file(s) remaining\rCompleted 131.8 KiB/467.1 KiB (658.7 KiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/manifest.xml\nCompleted 131.8 KiB/467.1 KiB (658.7 KiB/s) with 3 file(s) remaining\rCompleted 193.9 KiB/467.1 KiB (934.1 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000615.png to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615.png\nCompleted 193.9 KiB/467.1 KiB (934.1 KiB/s) with 2 file(s) remaining\rCompleted 407.2 KiB/467.1 KiB (1.9 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000615.pdf to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615.pdf\nCompleted 407.2 KiB/467.1 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 467.1 KiB/467.1 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000615_url.xml to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/contents/BIOMD0000000615_url.xml\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (127.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64711b3249c0d898ffdf07e1/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000615_url.sedml\ncreating dataset /BIOMD0000000615_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\ndataset created, uuid: d-1ea9c067-76b08d07-dc9b-6cd98b-8acf6f, chunk_size: (5, 1001)\ncreating dataset /BIOMD0000000615_url.sedml/autogen_report_for_task1, shape: (35, 1001), type: float64\ndataset created, uuid: d-1ea9c067-76b08d07-c6f9-c6d472-14aee9, chunk_size: (35, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000615_url.sedml\ncreating attribute uri in /BIOMD0000000615_url.sedml\ncreating attribute _type in /BIOMD0000000615_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000615_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000615_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000615_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000615_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000615_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000615_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000615_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000615_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000615_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000615_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000615_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000615_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000615_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000615_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000615_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000615_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000615_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000615_url.sedml\ncreate_links: /BIOMD0000000615_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000615_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000615_url.sedml/autogen_plot_for_task1, shape: (5, 1001), type: float64\niterating over chunks for /BIOMD0000000615_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000615_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000615_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000615_url.sedml/autogen_report_for_task1, shape: (35, 1001), type: float64\niterating over chunks for /BIOMD0000000615_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 35, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000615_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64711b3249c0d898ffdf07e1\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 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 and upload the outputs of the simulation run ... 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":18.985148,"sedDocuments":[{"location":"BIOMD0000000615_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  BIOMD0000000615_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: 4 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000615_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":18.657345,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":17.955664,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.302255,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_As","status":"SUCCEEDED"},{"id":"autogen_task1_Bs","status":"SUCCEEDED"},{"id":"autogen_task1_Asyn","status":"SUCCEEDED"},{"id":"autogen_task1_Bsyn","status":"SUCCEEDED"},{"id":"autogen_task1_nA","status":"SUCCEEDED"},{"id":"autogen_task1_k1","status":"SUCCEEDED"},{"id":"autogen_task1_k2","status":"SUCCEEDED"},{"id":"autogen_task1_qA","status":"SUCCEEDED"},{"id":"autogen_task1_QBs","status":"SUCCEEDED"},{"id":"autogen_task1_QBsyn","status":"SUCCEEDED"},{"id":"autogen_task1_TAh1","status":"SUCCEEDED"},{"id":"autogen_task1_TBh1","status":"SUCCEEDED"},{"id":"autogen_task1_Vs","status":"SUCCEEDED"},{"id":"autogen_task1_Vsyn","status":"SUCCEEDED"},{"id":"autogen_task1_t1","status":"SUCCEEDED"},{"id":"autogen_task1_t2","status":"SUCCEEDED"},{"id":"autogen_task1_default_compartment","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_R8","status":"SUCCEEDED"},{"id":"autogen_task1_R9","status":"SUCCEEDED"},{"id":"autogen_task1_R10","status":"SUCCEEDED"},{"id":"autogen_task1_R11","status":"SUCCEEDED"},{"id":"autogen_task1_R12","status":"SUCCEEDED"},{"id":"autogen_task1_R13","status":"SUCCEEDED"},{"id":"autogen_task1_R14","status":"SUCCEEDED"},{"id":"autogen_task1_R15","status":"SUCCEEDED"},{"id":"autogen_task1_R16","status":"SUCCEEDED"},{"id":"autogen_task1_R17","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.269809,"curves":[{"id":"autogen_curve_task1_As","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Bs","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Asyn","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Bsyn","status":"SUCCEEDED"}]}]}]}