{"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    329      0 --:--:-- --:--:-- --:--:--   330\n\r100  170k  100  170k    0     0   319k      0 --:--:-- --:--:-- --:--:--  319k\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 (20.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/rawLog.txt\nCompleted 5.9 KiB/5.9 KiB (68.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 85%)\n  adding: outputs/BIOMD0000000508_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000508_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)\n  adding: outputs/reports.h5 (deflated 23%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 141.6 KiB/141.6 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/outputs/reports.h5\nCompleted 121.2 KiB/146.3 KiB (1.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/output.zip\nCompleted 121.2 KiB/146.3 KiB (1.2 MiB/s) with 3 file(s) remaining\rCompleted 123.8 KiB/146.3 KiB (1.0 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/rawLog.txt\nCompleted 123.8 KiB/146.3 KiB (1.0 MiB/s) with 2 file(s) remaining\rCompleted 137.0 KiB/146.3 KiB (900.3 KiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000508_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/outputs/BIOMD0000000508_url.sedml/autogen_plot_for_task1.pdf\nCompleted 137.0 KiB/146.3 KiB (900.3 KiB/s) with 1 file(s) remaining\rCompleted 146.3 KiB/146.3 KiB (857.9 KiB/s) with 1 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/outputs/plots.zip\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000508-biopax2.owl  \n  inflating: contents/BIOMD0000000508-biopax3.owl  \n  inflating: contents/BIOMD0000000508-matlab.m  \n  inflating: contents/BIOMD0000000508-octave.m  \n  inflating: contents/BIOMD0000000508.m  \n  inflating: contents/BIOMD0000000508.ode  \n  inflating: contents/BIOMD0000000508.pdf  \n  inflating: contents/BIOMD0000000508.png  \n  inflating: contents/BIOMD0000000508.svg  \n  inflating: contents/BIOMD0000000508_url.sedml  \n  inflating: contents/BIOMD0000000508_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 9.1 KiB/318.2 KiB (125.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000508-biopax2.owl to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508-biopax2.owl\nCompleted 9.1 KiB/318.2 KiB (125.0 KiB/s) with 14 file(s) remaining\rCompleted 18.0 KiB/318.2 KiB (153.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000508-matlab.m to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508-matlab.m\nCompleted 18.0 KiB/318.2 KiB (153.1 KiB/s) with 13 file(s) remaining\rCompleted 26.8 KiB/318.2 KiB (225.8 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000508-octave.m to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508-octave.m\nCompleted 26.8 KiB/318.2 KiB (225.8 KiB/s) with 12 file(s) remaining\rCompleted 31.9 KiB/318.2 KiB (235.9 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000508.png to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508.png\nCompleted 31.9 KiB/318.2 KiB (235.9 KiB/s) with 11 file(s) remaining\rCompleted 32.7 KiB/318.2 KiB (222.7 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000508.svg to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508.svg\nCompleted 32.7 KiB/318.2 KiB (222.7 KiB/s) with 10 file(s) remaining\rCompleted 34.4 KiB/318.2 KiB (201.1 KiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/manifest.xml\nCompleted 34.4 KiB/318.2 KiB (201.1 KiB/s) with 9 file(s) remaining\rCompleted 65.3 KiB/318.2 KiB (369.9 KiB/s) with 9 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/curation_image.png\nCompleted 65.3 KiB/318.2 KiB (369.9 KiB/s) with 8 file(s) remaining\rCompleted 76.0 KiB/318.2 KiB (425.0 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000508-biopax3.owl to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508-biopax3.owl\nCompleted 76.0 KiB/318.2 KiB (425.0 KiB/s) with 7 file(s) remaining\rCompleted 110.8 KiB/318.2 KiB (605.8 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000508_url.sedml to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508_url.sedml\nCompleted 110.8 KiB/318.2 KiB (605.8 KiB/s) with 6 file(s) remaining\rCompleted 118.9 KiB/318.2 KiB (600.8 KiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000508.m to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508.m\nCompleted 118.9 KiB/318.2 KiB (600.8 KiB/s) with 5 file(s) remaining\rCompleted 151.7 KiB/318.2 KiB (757.6 KiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000508_url.xml to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508_url.xml\nCompleted 151.7 KiB/318.2 KiB (757.6 KiB/s) with 4 file(s) remaining\rCompleted 306.3 KiB/318.2 KiB (1.5 MiB/s) with 4 file(s) remaining  \rupload: contents/BIOMD0000000508.pdf to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508.pdf\nCompleted 306.3 KiB/318.2 KiB (1.5 MiB/s) with 3 file(s) remaining\rCompleted 306.5 KiB/318.2 KiB (1.5 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/curation_notes.txt\nCompleted 306.5 KiB/318.2 KiB (1.5 MiB/s) with 2 file(s) remaining\rCompleted 312.3 KiB/318.2 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000508.ode to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/BIOMD0000000508.ode\nCompleted 312.3 KiB/318.2 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 318.2 KiB/318.2 KiB (1.2 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/contents/metadata.rdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (85.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647110cd49c0d898ffdede16/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000508_url.sedml\ncreating dataset /BIOMD0000000508_url.sedml/autogen_plot_for_task1, shape: (17, 1001), type: float64\ndataset created, uuid: d-fd147de2-a244a2aa-d928-ff5706-4b315b, chunk_size: (17, 1001)\ncreating dataset /BIOMD0000000508_url.sedml/autogen_report_for_task1, shape: (66, 1001), type: float64\ndataset created, uuid: d-fd147de2-a244a2aa-7e79-aac2ec-4c7590, chunk_size: (66, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000508_url.sedml\ncreating attribute uri in /BIOMD0000000508_url.sedml\ncreating attribute _type in /BIOMD0000000508_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000508_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000508_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000508_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000508_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000508_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000508_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000508_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000508_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000508_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000508_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000508_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000508_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000508_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000508_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000508_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000508_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000508_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000508_url.sedml\ncreate_links: /BIOMD0000000508_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000508_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000508_url.sedml/autogen_plot_for_task1, shape: (17, 1001), type: float64\niterating over chunks for /BIOMD0000000508_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 17, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000508_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000508_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000508_url.sedml/autogen_report_for_task1, shape: (66, 1001), type: float64\niterating over chunks for /BIOMD0000000508_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 66, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000508_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647110cd49c0d898ffdede16\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve 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 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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.848033,"sedDocuments":[{"location":"BIOMD0000000508_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  BIOMD0000000508_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 66 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 16 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000508_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":1.388036,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.170392,"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":0.433038,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_d","status":"SUCCEEDED"},{"id":"autogen_task1_ad","status":"SUCCEEDED"},{"id":"autogen_task1_e","status":"SUCCEEDED"},{"id":"autogen_task1_r","status":"SUCCEEDED"},{"id":"autogen_task1_rs","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_ip3","status":"SUCCEEDED"},{"id":"autogen_task1_kg","status":"SUCCEEDED"},{"id":"autogen_task1_gstar","status":"SUCCEEDED"},{"id":"autogen_task1_ro","status":"SUCCEEDED"},{"id":"autogen_task1_ip3con","status":"SUCCEEDED"},{"id":"autogen_task1_dcon","status":"SUCCEEDED"},{"id":"autogen_task1_atp","status":"SUCCEEDED"},{"id":"autogen_task1_y","status":"SUCCEEDED"},{"id":"autogen_task1_delta","status":"SUCCEEDED"},{"id":"autogen_task1_ca","status":"SUCCEEDED"},{"id":"autogen_task1_addash","status":"SUCCEEDED"},{"id":"autogen_task1_vatp_s","status":"SUCCEEDED"},{"id":"autogen_task1_smoothness","status":"SUCCEEDED"},{"id":"autogen_task1_vdeg","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_ae","status":"SUCCEEDED"},{"id":"autogen_task1_ax","status":"SUCCEEDED"},{"id":"autogen_task1_k","status":"SUCCEEDED"},{"id":"autogen_task1_qd","status":"SUCCEEDED"},{"id":"autogen_task1_qe","status":"SUCCEEDED"},{"id":"autogen_task1_qx","status":"SUCCEEDED"},{"id":"autogen_task1_f","status":"SUCCEEDED"},{"id":"autogen_task1_g","status":"SUCCEEDED"},{"id":"autogen_task1_ps","status":"SUCCEEDED"},{"id":"autogen_task1_pd","status":"SUCCEEDED"},{"id":"autogen_task1_pe","status":"SUCCEEDED"},{"id":"autogen_task1_px","status":"SUCCEEDED"},{"id":"autogen_task1_ddd","status":"SUCCEEDED"},{"id":"autogen_task1_dee","status":"SUCCEEDED"},{"id":"autogen_task1_dxx","status":"SUCCEEDED"},{"id":"autogen_task1_af","status":"SUCCEEDED"},{"id":"autogen_task1_rt","status":"SUCCEEDED"},{"id":"autogen_task1_yo","status":"SUCCEEDED"},{"id":"autogen_task1_gf","status":"SUCCEEDED"},{"id":"autogen_task1_kdeg","status":"SUCCEEDED"},{"id":"autogen_task1_kkdeg","status":"SUCCEEDED"},{"id":"autogen_task1_ka","status":"SUCCEEDED"},{"id":"autogen_task1_kd","status":"SUCCEEDED"},{"id":"autogen_task1_rhstar","status":"SUCCEEDED"},{"id":"autogen_task1_dip","status":"SUCCEEDED"},{"id":"autogen_task1_krel","status":"SUCCEEDED"},{"id":"autogen_task1_ip3min","status":"SUCCEEDED"},{"id":"autogen_task1_datpp","status":"SUCCEEDED"},{"id":"autogen_task1_kr","status":"SUCCEEDED"},{"id":"autogen_task1_scale","status":"SUCCEEDED"},{"id":"autogen_task1_dcrit","status":"SUCCEEDED"},{"id":"autogen_task1_ymax","status":"SUCCEEDED"},{"id":"autogen_task1_cabasil","status":"SUCCEEDED"},{"id":"autogen_task1_p1","status":"SUCCEEDED"},{"id":"autogen_task1_p2","status":"SUCCEEDED"},{"id":"autogen_task1_p3","status":"SUCCEEDED"},{"id":"autogen_task1_p4","status":"SUCCEEDED"},{"id":"autogen_task1_p5","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_dist","status":"SUCCEEDED"},{"id":"autogen_task1_ip30","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.607906,"curves":[{"id":"autogen_curve_task1_d","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ad","status":"SUCCEEDED"},{"id":"autogen_curve_task1_e","status":"SUCCEEDED"},{"id":"autogen_curve_task1_r","status":"SUCCEEDED"},{"id":"autogen_curve_task1_rs","status":"SUCCEEDED"},{"id":"autogen_curve_task1_x","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ip3","status":"SUCCEEDED"},{"id":"autogen_curve_task1_kg","status":"SUCCEEDED"},{"id":"autogen_curve_task1_gstar","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ro","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ip3con","status":"SUCCEEDED"},{"id":"autogen_curve_task1_dcon","status":"SUCCEEDED"},{"id":"autogen_curve_task1_atp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_delta","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ca","status":"SUCCEEDED"}]}]}]}