{"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    450      0 --:--:-- --:--:-- --:--:--   451\n\r  0  787k    0   581    0     0   1317      0  0:10:12 --:--:--  0:10:12  1317\r100  787k  100  787k    0     0  1644k      0 --:--:-- --:--:-- --:--:-- 20.7M\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 (24.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/rawLog.txt\nCompleted 5.6 KiB/5.6 KiB (56.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 84%)\n  adding: outputs/BIOMD0000000015_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000015_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/reports.h5 (deflated 8%)\n  adding: rawLog.txt (deflated 70%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/327.8 KiB (4.6 MiB/s) with 1 file(s) remaining\rCompleted 327.8 KiB/327.8 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/outputs/reports.h5\nCompleted 256.0 KiB/337.9 KiB (5.9 MiB/s) with 4 file(s) remaining\rCompleted 314.1 KiB/337.9 KiB (3.2 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/output.zip\nCompleted 314.1 KiB/337.9 KiB (3.2 MiB/s) with 3 file(s) remaining\rCompleted 322.6 KiB/337.9 KiB (2.8 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/outputs/plots.zip\nCompleted 322.6 KiB/337.9 KiB (2.8 MiB/s) with 2 file(s) remaining\rCompleted 325.3 KiB/337.9 KiB (2.6 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/rawLog.txt\nCompleted 325.3 KiB/337.9 KiB (2.6 MiB/s) with 1 file(s) remaining\rCompleted 337.9 KiB/337.9 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000015_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/outputs/BIOMD0000000015_url.sedml/autogen_plot_for_task1.pdf\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000015-biopax2.owl  \n  inflating: contents/BIOMD0000000015-biopax3.owl  \n  inflating: contents/BIOMD0000000015-matlab.m  \n  inflating: contents/BIOMD0000000015-octave.m  \n  inflating: contents/BIOMD0000000015.m  \n  inflating: contents/BIOMD0000000015.ode  \n  inflating: contents/BIOMD0000000015.pdf  \n  inflating: contents/BIOMD0000000015.png  \n  inflating: contents/BIOMD0000000015.sci  \n  inflating: contents/BIOMD0000000015.svg  \n  inflating: contents/BIOMD0000000015_url.sedml  \n  inflating: contents/BIOMD0000000015_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 18.2 KiB/1.4 MiB (236.4 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000015-octave.m to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015-octave.m\nCompleted 18.2 KiB/1.4 MiB (236.4 KiB/s) with 15 file(s) remaining\rCompleted 36.4 KiB/1.4 MiB (282.1 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000015-matlab.m to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015-matlab.m\nCompleted 36.4 KiB/1.4 MiB (282.1 KiB/s) with 14 file(s) remaining\rCompleted 133.1 KiB/1.4 MiB (995.3 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000015-biopax2.owl to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015-biopax2.owl\nCompleted 133.1 KiB/1.4 MiB (995.3 KiB/s) with 13 file(s) remaining\rCompleted 389.1 KiB/1.4 MiB (2.7 MiB/s) with 13 file(s) remaining  \rCompleted 401.9 KiB/1.4 MiB (2.7 MiB/s) with 13 file(s) remaining  \rupload: contents/BIOMD0000000015.ode to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015.ode\nCompleted 401.9 KiB/1.4 MiB (2.7 MiB/s) with 12 file(s) remaining\rCompleted 420.1 KiB/1.4 MiB (2.6 MiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000015.m to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015.m\nCompleted 420.1 KiB/1.4 MiB (2.6 MiB/s) with 11 file(s) remaining\rCompleted 547.2 KiB/1.4 MiB (3.2 MiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000015-biopax3.owl to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015-biopax3.owl\nCompleted 547.2 KiB/1.4 MiB (3.2 MiB/s) with 10 file(s) remaining\rCompleted 549.0 KiB/1.4 MiB (3.1 MiB/s) with 10 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/manifest.xml\nCompleted 549.0 KiB/1.4 MiB (3.1 MiB/s) with 9 file(s) remaining\rCompleted 805.0 KiB/1.4 MiB (4.5 MiB/s) with 9 file(s) remaining\rCompleted 1.0 MiB/1.4 MiB (5.7 MiB/s) with 9 file(s) remaining  \rCompleted 1.1 MiB/1.4 MiB (5.6 MiB/s) with 9 file(s) remaining  \rupload: contents/BIOMD0000000015.pdf to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015.pdf\nCompleted 1.1 MiB/1.4 MiB (5.6 MiB/s) with 8 file(s) remaining\rCompleted 1.1 MiB/1.4 MiB (5.7 MiB/s) with 8 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/curation_image.png\nCompleted 1.1 MiB/1.4 MiB (5.7 MiB/s) with 7 file(s) remaining\rCompleted 1.1 MiB/1.4 MiB (5.4 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/metadata.rdf\nCompleted 1.1 MiB/1.4 MiB (5.4 MiB/s) with 6 file(s) remaining\rCompleted 1.1 MiB/1.4 MiB (5.4 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000015_url.sedml to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015_url.sedml\nCompleted 1.1 MiB/1.4 MiB (5.4 MiB/s) with 5 file(s) remaining\rCompleted 1.2 MiB/1.4 MiB (5.4 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000015.sci to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015.sci\nCompleted 1.2 MiB/1.4 MiB (5.4 MiB/s) with 4 file(s) remaining\rCompleted 1.2 MiB/1.4 MiB (5.7 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000015_url.xml to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015_url.xml\nCompleted 1.2 MiB/1.4 MiB (5.7 MiB/s) with 3 file(s) remaining\rCompleted 1.2 MiB/1.4 MiB (5.6 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/curation_notes.txt\nCompleted 1.2 MiB/1.4 MiB (5.6 MiB/s) with 2 file(s) remaining\rCompleted 1.3 MiB/1.4 MiB (5.4 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000015.png to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015.png\nCompleted 1.3 MiB/1.4 MiB (5.4 MiB/s) with 1 file(s) remaining\rCompleted 1.4 MiB/1.4 MiB (5.2 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000015.svg to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/contents/BIOMD0000000015.svg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.1 KiB/9.1 KiB (125.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647107210dcacb55678b37a5/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000015_url.sedml\ncreating dataset /BIOMD0000000015_url.sedml/autogen_plot_for_task1, shape: (19, 1001), type: float64\ndataset created, uuid: d-7e91e112-27134d8f-eb66-242080-225a5a, chunk_size: (19, 1001)\ncreating dataset /BIOMD0000000015_url.sedml/autogen_report_for_task1, shape: (57, 1001), type: float64\ndataset created, uuid: d-7e91e112-27134d8f-9c39-40e5ed-192096, chunk_size: (57, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000015_url.sedml\ncreating attribute uri in /BIOMD0000000015_url.sedml\ncreating attribute _type in /BIOMD0000000015_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000015_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000015_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000015_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000015_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000015_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000015_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000015_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000015_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000015_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000015_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000015_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000015_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000015_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000015_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000015_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000015_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000015_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000015_url.sedml\ncreate_links: /BIOMD0000000015_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000015_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000015_url.sedml/autogen_plot_for_task1, shape: (19, 1001), type: float64\niterating over chunks for /BIOMD0000000015_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 19, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000015_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000015_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000015_url.sedml/autogen_report_for_task1, shape: (57, 1001), type: float64\niterating over chunks for /BIOMD0000000015_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 57, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000015_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647107210dcacb55678b37a5\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 and upload the outputs of the simulation run ... 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.\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":2.12623,"sedDocuments":[{"location":"BIOMD0000000015_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  BIOMD0000000015_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 57 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 18 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000015_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":1.632912,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.302608,"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":0.460101,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_PRPP","status":"SUCCEEDED"},{"id":"autogen_task1_IMP","status":"SUCCEEDED"},{"id":"autogen_task1_SAMP","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_SAM","status":"SUCCEEDED"},{"id":"autogen_task1_Ade","status":"SUCCEEDED"},{"id":"autogen_task1_XMP","status":"SUCCEEDED"},{"id":"autogen_task1_GTP","status":"SUCCEEDED"},{"id":"autogen_task1_dATP","status":"SUCCEEDED"},{"id":"autogen_task1_dGTP","status":"SUCCEEDED"},{"id":"autogen_task1_RNA","status":"SUCCEEDED"},{"id":"autogen_task1_DNA","status":"SUCCEEDED"},{"id":"autogen_task1_HX","status":"SUCCEEDED"},{"id":"autogen_task1_Xa","status":"SUCCEEDED"},{"id":"autogen_task1_Gua","status":"SUCCEEDED"},{"id":"autogen_task1_UA","status":"SUCCEEDED"},{"id":"autogen_task1_R5P","status":"SUCCEEDED"},{"id":"autogen_task1_Pi","status":"SUCCEEDED"},{"id":"autogen_task1_cell","status":"SUCCEEDED"},{"id":"autogen_task1_ada","status":"SUCCEEDED"},{"id":"autogen_task1_ade","status":"SUCCEEDED"},{"id":"autogen_task1_adna","status":"SUCCEEDED"},{"id":"autogen_task1_adrnr","status":"SUCCEEDED"},{"id":"autogen_task1_ampd","status":"SUCCEEDED"},{"id":"autogen_task1_aprt","status":"SUCCEEDED"},{"id":"autogen_task1_arna","status":"SUCCEEDED"},{"id":"autogen_task1_asuc","status":"SUCCEEDED"},{"id":"autogen_task1_asli","status":"SUCCEEDED"},{"id":"autogen_task1_dada","status":"SUCCEEDED"},{"id":"autogen_task1_den","status":"SUCCEEDED"},{"id":"autogen_task1_dgnuc","status":"SUCCEEDED"},{"id":"autogen_task1_dnaa","status":"SUCCEEDED"},{"id":"autogen_task1_dnag","status":"SUCCEEDED"},{"id":"autogen_task1_gdna","status":"SUCCEEDED"},{"id":"autogen_task1_gdrnr","status":"SUCCEEDED"},{"id":"autogen_task1_gmpr","status":"SUCCEEDED"},{"id":"autogen_task1_gmps","status":"SUCCEEDED"},{"id":"autogen_task1_gnuc","status":"SUCCEEDED"},{"id":"autogen_task1_gprt","status":"SUCCEEDED"},{"id":"autogen_task1_grna","status":"SUCCEEDED"},{"id":"autogen_task1_gua","status":"SUCCEEDED"},{"id":"autogen_task1_hprt","status":"SUCCEEDED"},{"id":"autogen_task1_hx","status":"SUCCEEDED"},{"id":"autogen_task1_hxd","status":"SUCCEEDED"},{"id":"autogen_task1_impd","status":"SUCCEEDED"},{"id":"autogen_task1_inuc","status":"SUCCEEDED"},{"id":"autogen_task1_mat","status":"SUCCEEDED"},{"id":"autogen_task1_polyam","status":"SUCCEEDED"},{"id":"autogen_task1_prpps","status":"SUCCEEDED"},{"id":"autogen_task1_pyr","status":"SUCCEEDED"},{"id":"autogen_task1_rnaa","status":"SUCCEEDED"},{"id":"autogen_task1_rnag","status":"SUCCEEDED"},{"id":"autogen_task1_trans","status":"SUCCEEDED"},{"id":"autogen_task1_ua","status":"SUCCEEDED"},{"id":"autogen_task1_x","status":"SUCCEEDED"},{"id":"autogen_task1_xd","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.685692,"curves":[{"id":"autogen_curve_task1_PRPP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IMP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_SAMP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_SAM","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ade","status":"SUCCEEDED"},{"id":"autogen_curve_task1_XMP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GTP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_dATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_dGTP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_RNA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DNA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_HX","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Xa","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Gua","status":"SUCCEEDED"},{"id":"autogen_curve_task1_UA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R5P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pi","status":"SUCCEEDED"}]}]}]}