{"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    497      0 --:--:-- --:--:-- --:--:--   498\n\r100  267k  100  267k    0     0   660k      0 --:--:-- --:--:-- --:--:--  660k\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 (25.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (58.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000263_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000263_url.sedml/autogen_plot_for_task1.pdf (deflated 32%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/264.5 KiB (5.9 MiB/s) with 1 file(s) remaining\rCompleted 264.5 KiB/264.5 KiB (3.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/outputs/reports.h5\nCompleted 245.0 KiB/264.8 KiB (2.3 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/output.zip\nCompleted 245.0 KiB/264.8 KiB (2.3 MiB/s) with 3 file(s) remaining\rCompleted 247.7 KiB/264.8 KiB (2.3 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/rawLog.txt\nCompleted 247.7 KiB/264.8 KiB (2.3 MiB/s) with 2 file(s) remaining\rCompleted 258.0 KiB/264.8 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000263_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/outputs/BIOMD0000000263_url.sedml/autogen_plot_for_task1.pdf\nCompleted 258.0 KiB/264.8 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 264.8 KiB/264.8 KiB (1.7 MiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000263-biopax2.owl  \n  inflating: contents/BIOMD0000000263-biopax3.owl  \n  inflating: contents/BIOMD0000000263-matlab.m  \n  inflating: contents/BIOMD0000000263-octave.m  \n  inflating: contents/BIOMD0000000263.m  \n  inflating: contents/BIOMD0000000263.pdf  \n  inflating: contents/BIOMD0000000263.png  \n  inflating: contents/BIOMD0000000263.svg  \n  inflating: contents/BIOMD0000000263_url.sedml  \n  inflating: contents/BIOMD0000000263_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 33.8 KiB/488.6 KiB (461.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000263-biopax3.owl to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/BIOMD0000000263-biopax3.owl\nCompleted 33.8 KiB/488.6 KiB (461.1 KiB/s) with 13 file(s) remaining\rCompleted 41.5 KiB/488.6 KiB (398.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000263-matlab.m to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/BIOMD0000000263-matlab.m\nCompleted 41.5 KiB/488.6 KiB (398.5 KiB/s) with 12 file(s) remaining\rCompleted 64.1 KiB/488.6 KiB (489.5 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000263-biopax2.owl to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/BIOMD0000000263-biopax2.owl\nCompleted 64.1 KiB/488.6 KiB (489.5 KiB/s) with 11 file(s) remaining\rCompleted 71.8 KiB/488.6 KiB (520.2 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000263-octave.m to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/BIOMD0000000263-octave.m\nCompleted 71.8 KiB/488.6 KiB (520.2 KiB/s) with 10 file(s) remaining\rCompleted 93.2 KiB/488.6 KiB (662.3 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000263_url.sedml to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/BIOMD0000000263_url.sedml\nCompleted 93.2 KiB/488.6 KiB (662.3 KiB/s) with 9 file(s) remaining\rCompleted 147.7 KiB/488.6 KiB (1013.0 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/curation_image.png\nCompleted 147.7 KiB/488.6 KiB (1013.0 KiB/s) with 8 file(s) remaining\rCompleted 147.9 KiB/488.6 KiB (930.1 KiB/s) with 8 file(s) remaining \rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/curation_notes.txt\nCompleted 147.9 KiB/488.6 KiB (930.1 KiB/s) with 7 file(s) remaining\rCompleted 355.2 KiB/488.6 KiB (2.2 MiB/s) with 7 file(s) remaining  \rupload: contents/BIOMD0000000263.pdf to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/BIOMD0000000263.pdf\nCompleted 355.2 KiB/488.6 KiB (2.2 MiB/s) with 6 file(s) remaining\rCompleted 408.1 KiB/488.6 KiB (2.4 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000263.png to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/BIOMD0000000263.png\nCompleted 408.1 KiB/488.6 KiB (2.4 MiB/s) with 5 file(s) remaining\rCompleted 434.4 KiB/488.6 KiB (2.5 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000263.svg to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/BIOMD0000000263.svg\nCompleted 434.4 KiB/488.6 KiB (2.5 MiB/s) with 4 file(s) remaining\rCompleted 442.2 KiB/488.6 KiB (2.5 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000263.m to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/BIOMD0000000263.m\nCompleted 442.2 KiB/488.6 KiB (2.5 MiB/s) with 3 file(s) remaining\rCompleted 481.3 KiB/488.6 KiB (2.5 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000263_url.xml to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/BIOMD0000000263_url.xml\nCompleted 481.3 KiB/488.6 KiB (2.5 MiB/s) with 2 file(s) remaining\rCompleted 482.9 KiB/488.6 KiB (2.3 MiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/manifest.xml\nCompleted 482.9 KiB/488.6 KiB (2.3 MiB/s) with 1 file(s) remaining\rCompleted 488.6 KiB/488.6 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.2 KiB/8.2 KiB (117.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/64710a689a62a8be53f79cfe/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000263_url.sedml\ncreating dataset /BIOMD0000000263_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-c922e2cc-85d620be-3c4a-6a6d05-e30484, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000263_url.sedml/autogen_report_for_task1, shape: (36, 1001), type: float64\ndataset created, uuid: d-c922e2cc-85d620be-a3d0-92a8a5-85db93, chunk_size: (36, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000263_url.sedml\ncreating attribute uri in /BIOMD0000000263_url.sedml\ncreating attribute _type in /BIOMD0000000263_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000263_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000263_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000263_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000263_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000263_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000263_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000263_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000263_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000263_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000263_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000263_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000263_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000263_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000263_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000263_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000263_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000263_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000263_url.sedml\ncreate_links: /BIOMD0000000263_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000263_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000263_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000263_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000263_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000263_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000263_url.sedml/autogen_report_for_task1, shape: (36, 1001), type: float64\niterating over chunks for /BIOMD0000000263_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 36, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000263_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/64710a689a62a8be53f79cfe\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 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.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":18.066741,"sedDocuments":[{"location":"BIOMD0000000263_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  BIOMD0000000263_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 36 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000263_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":17.76452,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":16.969591,"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":0.286405,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_NGF","status":"SUCCEEDED"},{"id":"autogen_task1_TrkA","status":"SUCCEEDED"},{"id":"autogen_task1_pTrkA","status":"SUCCEEDED"},{"id":"autogen_task1_pTrkA_Akt","status":"SUCCEEDED"},{"id":"autogen_task1_Akt","status":"SUCCEEDED"},{"id":"autogen_task1_pAkt","status":"SUCCEEDED"},{"id":"autogen_task1_S6","status":"SUCCEEDED"},{"id":"autogen_task1_pAkt_S6","status":"SUCCEEDED"},{"id":"autogen_task1_pS6","status":"SUCCEEDED"},{"id":"autogen_task1_pro_TrkA","status":"SUCCEEDED"},{"id":"autogen_task1_NGF_TrkA","status":"SUCCEEDED"},{"id":"autogen_task1_pTrkA_total","status":"SUCCEEDED"},{"id":"autogen_task1_pAkt_total","status":"SUCCEEDED"},{"id":"autogen_task1_pTrkA_scaleFactor","status":"SUCCEEDED"},{"id":"autogen_task1_pAkt_scaleFactor","status":"SUCCEEDED"},{"id":"autogen_task1_pS6_scaleFactor","status":"SUCCEEDED"},{"id":"autogen_task1_pS6_total","status":"SUCCEEDED"},{"id":"autogen_task1_NGF_conc_step","status":"SUCCEEDED"},{"id":"autogen_task1_NGF_conc_pulse","status":"SUCCEEDED"},{"id":"autogen_task1_NGF_conc_ramp","status":"SUCCEEDED"},{"id":"autogen_task1_TrkA_turnover","status":"SUCCEEDED"},{"id":"autogen_task1_pulse_time","status":"SUCCEEDED"},{"id":"autogen_task1_ramp_time","status":"SUCCEEDED"},{"id":"autogen_task1_Cell","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_1","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_2","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_3","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_4","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_5","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_6","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_7","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_8","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_9","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_10","status":"SUCCEEDED"},{"id":"autogen_task1_reaction_11","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.380785,"curves":[{"id":"autogen_curve_task1_NGF","status":"SUCCEEDED"},{"id":"autogen_curve_task1_TrkA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pTrkA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pTrkA_Akt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Akt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pAkt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S6","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pAkt_S6","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pS6","status":"SUCCEEDED"},{"id":"autogen_curve_task1_pro_TrkA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NGF_TrkA","status":"SUCCEEDED"}]}]}]}