{"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\r100   139  100   139    0     0    444      0 --:--:-- --:--:-- --:--:--   445\n\r100  240k  100  240k    0     0   526k      0 --:--:-- --:--:-- --:--:--  526k\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 (24.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/rawLog.txt\nCompleted 2.7 KiB/2.7 KiB (26.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 75%)\n  adding: outputs/BIOMD0000000005.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000005.sedml/plot1.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 15%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 139.3 KiB/139.3 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/outputs/reports.h5\nCompleted 9.2 KiB/154.5 KiB (91.8 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/outputs/plots.zip\nCompleted 9.2 KiB/154.5 KiB (91.8 KiB/s) with 3 file(s) remaining\rCompleted 139.5 KiB/154.5 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/output.zip\nCompleted 139.5 KiB/154.5 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 142.1 KiB/154.5 KiB (816.8 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/rawLog.txt\nCompleted 142.1 KiB/154.5 KiB (816.8 KiB/s) with 1 file(s) remaining\rCompleted 154.5 KiB/154.5 KiB (644.0 KiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000005.sedml/plot1.pdf to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/outputs/BIOMD0000000005.sedml/plot1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000005-biopax2.owl  \n  inflating: contents/BIOMD0000000005-biopax3.owl  \n  inflating: contents/BIOMD0000000005-matlab.m  \n  inflating: contents/BIOMD0000000005-octave.m  \n  inflating: contents/BIOMD0000000005.m  \n  inflating: contents/BIOMD0000000005.ode  \n  inflating: contents/BIOMD0000000005.pdf  \n  inflating: contents/BIOMD0000000005.png  \n  inflating: contents/BIOMD0000000005.sci  \n  inflating: contents/BIOMD0000000005.sedml  \n  inflating: contents/BIOMD0000000005.svg  \n  inflating: contents/BIOMD0000000005.vcml  \n  inflating: contents/BIOMD0000000005_manual.png  \n  inflating: contents/BIOMD0000000005_manual.svg  \n  inflating: contents/BIOMD0000000005_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 29.5 KiB/465.2 KiB (316.8 KiB/s) with 19 file(s) remaining\rupload: contents/BIOMD0000000005-biopax3.owl to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005-biopax3.owl\nCompleted 29.5 KiB/465.2 KiB (316.8 KiB/s) with 18 file(s) remaining\rCompleted 32.5 KiB/465.2 KiB (225.1 KiB/s) with 18 file(s) remaining\rupload: contents/BIOMD0000000005.sci to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005.sci\nCompleted 32.5 KiB/465.2 KiB (225.1 KiB/s) with 17 file(s) remaining\rCompleted 38.1 KiB/465.2 KiB (231.6 KiB/s) with 17 file(s) remaining\rupload: contents/BIOMD0000000005-octave.m to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005-octave.m\nCompleted 38.1 KiB/465.2 KiB (231.6 KiB/s) with 16 file(s) remaining\rCompleted 48.9 KiB/465.2 KiB (291.6 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000005.sedml to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005.sedml\nCompleted 48.9 KiB/465.2 KiB (291.6 KiB/s) with 15 file(s) remaining\rCompleted 72.7 KiB/465.2 KiB (422.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000005.svg to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005.svg\nCompleted 72.7 KiB/465.2 KiB (422.7 KiB/s) with 14 file(s) remaining\rCompleted 78.3 KiB/465.2 KiB (408.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000005-matlab.m to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005-matlab.m\nCompleted 78.3 KiB/465.2 KiB (408.1 KiB/s) with 13 file(s) remaining\rCompleted 102.1 KiB/465.2 KiB (520.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000005_manual.svg to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005_manual.svg\nCompleted 102.1 KiB/465.2 KiB (520.8 KiB/s) with 12 file(s) remaining\rCompleted 134.6 KiB/465.2 KiB (670.2 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000005_manual.png to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005_manual.png\nCompleted 134.6 KiB/465.2 KiB (670.2 KiB/s) with 11 file(s) remaining\rCompleted 171.8 KiB/465.2 KiB (844.8 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000005.vcml to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005.vcml\nCompleted 171.8 KiB/465.2 KiB (844.8 KiB/s) with 10 file(s) remaining\rCompleted 173.9 KiB/465.2 KiB (761.1 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/manifest.xml\nCompleted 173.9 KiB/465.2 KiB (761.1 KiB/s) with 9 file(s) remaining\rCompleted 199.9 KiB/465.2 KiB (870.2 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000005_url.xml to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005_url.xml\nCompleted 199.9 KiB/465.2 KiB (870.2 KiB/s) with 8 file(s) remaining\rCompleted 221.5 KiB/465.2 KiB (877.1 KiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/curation_image.png\nCompleted 221.5 KiB/465.2 KiB (877.1 KiB/s) with 7 file(s) remaining\rCompleted 242.2 KiB/465.2 KiB (932.5 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000005-biopax2.owl to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005-biopax2.owl\nCompleted 242.2 KiB/465.2 KiB (932.5 KiB/s) with 6 file(s) remaining\rCompleted 247.9 KiB/465.2 KiB (943.3 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000005.m to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005.m\nCompleted 247.9 KiB/465.2 KiB (943.3 KiB/s) with 5 file(s) remaining\rCompleted 425.3 KiB/465.2 KiB (1.5 MiB/s) with 5 file(s) remaining  \rupload: contents/BIOMD0000000005.pdf to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005.pdf\nCompleted 425.3 KiB/465.2 KiB (1.5 MiB/s) with 4 file(s) remaining\rCompleted 425.4 KiB/465.2 KiB (1.5 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/curation_notes.txt\nCompleted 425.4 KiB/465.2 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 429.3 KiB/465.2 KiB (1.4 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/metadata.rdf\nCompleted 429.3 KiB/465.2 KiB (1.4 MiB/s) with 2 file(s) remaining\rCompleted 432.6 KiB/465.2 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000005.ode to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005.ode\nCompleted 432.6 KiB/465.2 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 465.2 KiB/465.2 KiB (1.5 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000005.png to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/contents/BIOMD0000000005.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.7 KiB/9.7 KiB (124.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647106fd9a62a8be53f734de/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000005.sedml\ncreating dataset /BIOMD0000000005.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\ndataset created, uuid: d-837401a4-3504ed76-edb9-dc7cad-c3c541, chunk_size: (20, 1001)\ncreating dataset /BIOMD0000000005.sedml/plot1, shape: (3, 1001), type: float64\ndataset created, uuid: d-837401a4-3504ed76-8816-3c50d1-9bb920, chunk_size: (3, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000005.sedml\ncreating attribute uri in /BIOMD0000000005.sedml\ncreating attribute _type in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000005.sedml/autogen_report_for_task1\ncreating attribute _type in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlDataSetIds in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlDataSetNames in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlId in /BIOMD0000000005.sedml/plot1\ncreating attribute sedmlName in /BIOMD0000000005.sedml/plot1\ncreating attribute uri in /BIOMD0000000005.sedml/plot1\ncreate_links: /\ngot link: BIOMD0000000005.sedml\ncreate_links: /BIOMD0000000005.sedml\ngot link: autogen_report_for_task1\ngot link: plot1\nwrite_dataset src: /BIOMD0000000005.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000005.sedml/autogen_report_for_task1, shape: (20, 1001), type: float64\niterating over chunks for /BIOMD0000000005.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 20, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000005.sedml/autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000005.sedml/plot1 to tgt: /BIOMD0000000005.sedml/plot1, shape: (3, 1001), type: float64\niterating over chunks for /BIOMD0000000005.sedml/plot1\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000005.sedml/plot1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647106fd9a62a8be53f734de\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 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 and upload the outputs of the simulation run ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":20.893399,"sedDocuments":[{"location":"BIOMD0000000005.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  BIOMD0000000005.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 20 data sets\r\n    Plots (1):\r\n      plot1: 2 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000005.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n    Outputs:\r\n      `autogen_report_for_task1`\r\n      `plot1`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `plot1` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task1` ...","duration":20.547134,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":19.970562,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"plot1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.245189,"curves":[{"id":"curve_0","status":"SUCCEEDED"},{"id":"curve_1","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.20232,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_YT","status":"SUCCEEDED"},{"id":"autogen_task1_M","status":"SUCCEEDED"},{"id":"autogen_task1_EmptySet","status":"SUCCEEDED"},{"id":"autogen_task1_C2","status":"SUCCEEDED"},{"id":"autogen_task1_CP","status":"SUCCEEDED"},{"id":"autogen_task1_pM","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_YP","status":"SUCCEEDED"},{"id":"autogen_task1_CT","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction1","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction2","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction3","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction4","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction5","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction6","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction7","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction8","status":"SUCCEEDED"},{"id":"autogen_task1_Reaction9","status":"SUCCEEDED"}]}]}]}