{"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    431      0 --:--:-- --:--:-- --:--:--   431\n\r100  238k  100  238k    0     0   530k      0 --:--:-- --:--:-- --:--:--  530k\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 (25.2 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/rawLog.txt\nCompleted 5.1 KiB/5.1 KiB (74.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/BIOMD0000000170_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000170_url.sedml/autogen_plot_for_task1.pdf (deflated 23%)\n  adding: outputs/reports.h5 (deflated 10%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/280.5 KiB (5.6 MiB/s) with 1 file(s) remaining\rCompleted 280.5 KiB/280.5 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/outputs/reports.h5\nCompleted 256.0 KiB/287.0 KiB (5.6 MiB/s) with 4 file(s) remaining\rCompleted 263.1 KiB/287.0 KiB (2.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/output.zip\nCompleted 263.1 KiB/287.0 KiB (2.7 MiB/s) with 3 file(s) remaining\rCompleted 272.2 KiB/287.0 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/outputs/plots.zip\nCompleted 272.2 KiB/287.0 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 284.3 KiB/287.0 KiB (2.5 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000170_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/outputs/BIOMD0000000170_url.sedml/autogen_plot_for_task1.pdf\nCompleted 284.3 KiB/287.0 KiB (2.5 MiB/s) with 1 file(s) remaining\rCompleted 287.0 KiB/287.0 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/rawLog.txt\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000170-biopax2.owl  \n  inflating: contents/BIOMD0000000170-biopax3.owl  \n  inflating: contents/BIOMD0000000170-matlab.m  \n  inflating: contents/BIOMD0000000170-octave.m  \n  inflating: contents/BIOMD0000000170.m  \n  inflating: contents/BIOMD0000000170.ode  \n  inflating: contents/BIOMD0000000170.pdf  \n  inflating: contents/BIOMD0000000170.png  \n  inflating: contents/BIOMD0000000170.svg  \n  inflating: contents/BIOMD0000000170_url.sedml  \n  inflating: contents/BIOMD0000000170_url.xml  \n  inflating: contents/curation_image.jpeg  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 8.5 KiB/472.3 KiB (75.8 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000170-octave.m to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170-octave.m\nCompleted 8.5 KiB/472.3 KiB (75.8 KiB/s) with 14 file(s) remaining\rCompleted 17.0 KiB/472.3 KiB (135.5 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000170-matlab.m to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170-matlab.m\nCompleted 17.0 KiB/472.3 KiB (135.5 KiB/s) with 13 file(s) remaining\rCompleted 39.3 KiB/472.3 KiB (300.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000170-biopax2.owl to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170-biopax2.owl\nCompleted 39.3 KiB/472.3 KiB (300.9 KiB/s) with 12 file(s) remaining\rCompleted 104.4 KiB/472.3 KiB (752.1 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000170.png to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170.png\nCompleted 104.4 KiB/472.3 KiB (752.1 KiB/s) with 11 file(s) remaining\rCompleted 139.8 KiB/472.3 KiB (991.0 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000170.svg to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170.svg\nCompleted 139.8 KiB/472.3 KiB (991.0 KiB/s) with 10 file(s) remaining\rCompleted 170.1 KiB/472.3 KiB (1001.5 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000170_url.sedml to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170_url.sedml\nCompleted 170.1 KiB/472.3 KiB (1001.5 KiB/s) with 9 file(s) remaining\rCompleted 195.3 KiB/472.3 KiB (1.1 MiB/s) with 9 file(s) remaining   \rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/curation_image.jpeg\nCompleted 195.3 KiB/472.3 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 196.9 KiB/472.3 KiB (1.1 MiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/metadata.rdf\nCompleted 196.9 KiB/472.3 KiB (1.1 MiB/s) with 7 file(s) remaining\rCompleted 196.9 KiB/472.3 KiB (1.1 MiB/s) with 7 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/curation_notes.txt\nCompleted 196.9 KiB/472.3 KiB (1.1 MiB/s) with 6 file(s) remaining\rCompleted 198.7 KiB/472.3 KiB (1.1 MiB/s) with 6 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/manifest.xml\nCompleted 198.7 KiB/472.3 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 230.4 KiB/472.3 KiB (1.2 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000170_url.xml to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170_url.xml\nCompleted 230.4 KiB/472.3 KiB (1.2 MiB/s) with 4 file(s) remaining\rCompleted 264.2 KiB/472.3 KiB (1.3 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000170-biopax3.owl to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170-biopax3.owl\nCompleted 264.2 KiB/472.3 KiB (1.3 MiB/s) with 3 file(s) remaining\rCompleted 458.2 KiB/472.3 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000170.pdf to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170.pdf\nCompleted 458.2 KiB/472.3 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 463.8 KiB/472.3 KiB (2.2 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000170.ode to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170.ode\nCompleted 463.8 KiB/472.3 KiB (2.2 MiB/s) with 1 file(s) remaining\rCompleted 472.3 KiB/472.3 KiB (2.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000170.m to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/contents/BIOMD0000000170.m\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.7 KiB/8.7 KiB (124.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109239a62a8be53f775b4/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000170_url.sedml\ncreating dataset /BIOMD0000000170_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-4e36b1ed-1f6af834-310a-9feb53-06c4c3, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000170_url.sedml/autogen_report_for_task1, shape: (54, 1001), type: float64\ndataset created, uuid: d-4e36b1ed-1f6af834-abeb-3660b1-10eccf, chunk_size: (54, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000170_url.sedml\ncreating attribute uri in /BIOMD0000000170_url.sedml\ncreating attribute _type in /BIOMD0000000170_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000170_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000170_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000170_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000170_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000170_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000170_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000170_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000170_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000170_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000170_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000170_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000170_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000170_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000170_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000170_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000170_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000170_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000170_url.sedml\ncreate_links: /BIOMD0000000170_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000170_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000170_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000170_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000170_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000170_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000170_url.sedml/autogen_report_for_task1, shape: (54, 1001), type: float64\niterating over chunks for /BIOMD0000000170_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 54, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000170_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647109239a62a8be53f775b4\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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":23.062028,"sedDocuments":[{"location":"BIOMD0000000170_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  BIOMD0000000170_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 54 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000170_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":22.692712,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":21.751756,"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":0.453566,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_y1","status":"SUCCEEDED"},{"id":"autogen_task1_y2","status":"SUCCEEDED"},{"id":"autogen_task1_y3","status":"SUCCEEDED"},{"id":"autogen_task1_y4","status":"SUCCEEDED"},{"id":"autogen_task1_y5","status":"SUCCEEDED"},{"id":"autogen_task1_y6","status":"SUCCEEDED"},{"id":"autogen_task1_y7","status":"SUCCEEDED"},{"id":"autogen_task1_trans_per2_cry","status":"SUCCEEDED"},{"id":"autogen_task1_v1b","status":"SUCCEEDED"},{"id":"autogen_task1_c","status":"SUCCEEDED"},{"id":"autogen_task1_k1b","status":"SUCCEEDED"},{"id":"autogen_task1_k1i","status":"SUCCEEDED"},{"id":"autogen_task1_hill_coeff","status":"SUCCEEDED"},{"id":"autogen_task1_trans_Bmal1","status":"SUCCEEDED"},{"id":"autogen_task1_v4b","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_k4b","status":"SUCCEEDED"},{"id":"autogen_task1_y5_y6_y7","status":"SUCCEEDED"},{"id":"autogen_task1_k1d","status":"SUCCEEDED"},{"id":"autogen_task1_k2b","status":"SUCCEEDED"},{"id":"autogen_task1_q","status":"SUCCEEDED"},{"id":"autogen_task1_k2d","status":"SUCCEEDED"},{"id":"autogen_task1_k2t","status":"SUCCEEDED"},{"id":"autogen_task1_k3t","status":"SUCCEEDED"},{"id":"autogen_task1_k3d","status":"SUCCEEDED"},{"id":"autogen_task1_k4d","status":"SUCCEEDED"},{"id":"autogen_task1_k5b","status":"SUCCEEDED"},{"id":"autogen_task1_k5d","status":"SUCCEEDED"},{"id":"autogen_task1_k5t","status":"SUCCEEDED"},{"id":"autogen_task1_k6t","status":"SUCCEEDED"},{"id":"autogen_task1_k6d","status":"SUCCEEDED"},{"id":"autogen_task1_k6a","status":"SUCCEEDED"},{"id":"autogen_task1_k7a","status":"SUCCEEDED"},{"id":"autogen_task1_k7d","status":"SUCCEEDED"},{"id":"autogen_task1_Nucleus","status":"SUCCEEDED"},{"id":"autogen_task1_Cytoplasm","status":"SUCCEEDED"},{"id":"autogen_task1_per2_cry_transcription","status":"SUCCEEDED"},{"id":"autogen_task1_per2_cry_mRNA_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_per2_cry_complex_formation","status":"SUCCEEDED"},{"id":"autogen_task1_cytoplasmic_per2_cry_complex_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_per2_cry_nuclear_import","status":"SUCCEEDED"},{"id":"autogen_task1_per2_cry_nuclear_export","status":"SUCCEEDED"},{"id":"autogen_task1_nuclear_per2_cry_complex_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_Bmal1_transcription","status":"SUCCEEDED"},{"id":"autogen_task1_Bmal1_mRNA_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_BMAL1_translation","status":"SUCCEEDED"},{"id":"autogen_task1_cytoplasmic_BMAL1_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_BMAL1_nuclear_import","status":"SUCCEEDED"},{"id":"autogen_task1_BMAL1_nuclear_export","status":"SUCCEEDED"},{"id":"autogen_task1_nuclear_BMAL1_degradation","status":"SUCCEEDED"},{"id":"autogen_task1_BMAL1_activation","status":"SUCCEEDED"},{"id":"autogen_task1_BMAL1_deactivation","status":"SUCCEEDED"},{"id":"autogen_task1_Active_BMAL1_degradation","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.324869,"curves":[{"id":"autogen_curve_task1_y1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y4","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y5","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y6","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y7","status":"SUCCEEDED"}]}]}]}