{"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    444      0 --:--:-- --:--:-- --:--:--   444\n\r100  226k  100  226k    0     0   520k      0 --:--:-- --:--:-- --:--:--  520k\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 (26.4 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/rawLog.txt\nCompleted 4.4 KiB/4.4 KiB (68.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/BIOMD0000000100_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000100_url.sedml/autogen_plot_for_task1.pdf (deflated 31%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/reports.h5 (deflated 18%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 156.6 KiB/156.6 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/outputs/reports.h5\nCompleted 136.9 KiB/155.6 KiB (1.6 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/output.zip\nCompleted 136.9 KiB/155.6 KiB (1.6 MiB/s) with 3 file(s) remaining\rCompleted 143.3 KiB/155.6 KiB (1.1 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/outputs/plots.zip\nCompleted 143.3 KiB/155.6 KiB (1.1 MiB/s) with 2 file(s) remaining\rCompleted 146.0 KiB/155.6 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/rawLog.txt\nCompleted 146.0 KiB/155.6 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 155.6 KiB/155.6 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000100_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/outputs/BIOMD0000000100_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/BIOMD0000000100-biopax2.owl  \n  inflating: contents/BIOMD0000000100-biopax3.owl  \n  inflating: contents/BIOMD0000000100-matlab.m  \n  inflating: contents/BIOMD0000000100-octave.m  \n  inflating: contents/BIOMD0000000100.m  \n  inflating: contents/BIOMD0000000100.ode  \n  inflating: contents/BIOMD0000000100.pdf  \n  inflating: contents/BIOMD0000000100.png  \n  inflating: contents/BIOMD0000000100.svg  \n  inflating: contents/BIOMD0000000100.vcml  \n  inflating: contents/BIOMD0000000100_url.sedml  \n  inflating: contents/BIOMD0000000100_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 25.0 KiB/441.9 KiB (340.0 KiB/s) with 16 file(s) remaining\rupload: contents/BIOMD0000000100-biopax3.owl to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100-biopax3.owl\nCompleted 25.0 KiB/441.9 KiB (340.0 KiB/s) with 15 file(s) remaining\rCompleted 31.7 KiB/441.9 KiB (289.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000100-matlab.m to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100-matlab.m\nCompleted 31.7 KiB/441.9 KiB (289.0 KiB/s) with 14 file(s) remaining\rCompleted 33.6 KiB/441.9 KiB (266.6 KiB/s) with 14 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/manifest.xml\nCompleted 33.6 KiB/441.9 KiB (266.6 KiB/s) with 13 file(s) remaining\rCompleted 40.3 KiB/441.9 KiB (289.7 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000100-octave.m to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100-octave.m\nCompleted 40.3 KiB/441.9 KiB (289.7 KiB/s) with 12 file(s) remaining\rCompleted 59.0 KiB/441.9 KiB (415.8 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000100-biopax2.owl to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100-biopax2.owl\nCompleted 59.0 KiB/441.9 KiB (415.8 KiB/s) with 11 file(s) remaining\rCompleted 94.5 KiB/441.9 KiB (656.5 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000100.vcml to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100.vcml\nCompleted 94.5 KiB/441.9 KiB (656.5 KiB/s) with 10 file(s) remaining\rCompleted 113.7 KiB/441.9 KiB (777.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000100.svg to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100.svg\nCompleted 113.7 KiB/441.9 KiB (777.8 KiB/s) with 9 file(s) remaining\rCompleted 138.7 KiB/441.9 KiB (934.7 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000100_url.sedml to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100_url.sedml\nCompleted 138.7 KiB/441.9 KiB (934.7 KiB/s) with 8 file(s) remaining\rCompleted 142.7 KiB/441.9 KiB (852.6 KiB/s) with 8 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/metadata.rdf\nCompleted 142.7 KiB/441.9 KiB (852.6 KiB/s) with 7 file(s) remaining\rCompleted 173.0 KiB/441.9 KiB (1021.8 KiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000100_url.xml to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100_url.xml\nCompleted 173.0 KiB/441.9 KiB (1021.8 KiB/s) with 6 file(s) remaining\rCompleted 186.6 KiB/441.9 KiB (1.1 MiB/s) with 6 file(s) remaining   \rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/curation_image.jpeg\nCompleted 186.6 KiB/441.9 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 186.7 KiB/441.9 KiB (1.0 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/curation_notes.txt\nCompleted 186.7 KiB/441.9 KiB (1.0 MiB/s) with 4 file(s) remaining\rCompleted 191.0 KiB/441.9 KiB (878.1 KiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000100.ode to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100.ode\nCompleted 191.0 KiB/441.9 KiB (878.1 KiB/s) with 3 file(s) remaining\rCompleted 197.7 KiB/441.9 KiB (890.8 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000100.m to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100.m\nCompleted 197.7 KiB/441.9 KiB (890.8 KiB/s) with 2 file(s) remaining\rCompleted 266.4 KiB/441.9 KiB (1.2 MiB/s) with 2 file(s) remaining  \rupload: contents/BIOMD0000000100.png to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100.png\nCompleted 266.4 KiB/441.9 KiB (1.2 MiB/s) with 1 file(s) remaining\rCompleted 441.9 KiB/441.9 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000100.pdf to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/contents/BIOMD0000000100.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.9 KiB/8.9 KiB (135.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6471084149c0d898ffddb249/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000100_url.sedml\ncreating dataset /BIOMD0000000100_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\ndataset created, uuid: d-cc1357e0-723926d9-7e2a-ffeae2-5a1c07, chunk_size: (6, 1001)\ncreating dataset /BIOMD0000000100_url.sedml/autogen_report_for_task1, shape: (49, 1001), type: float64\ndataset created, uuid: d-cc1357e0-723926d9-f753-80aeb1-c02ee6, chunk_size: (49, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000100_url.sedml\ncreating attribute uri in /BIOMD0000000100_url.sedml\ncreating attribute _type in /BIOMD0000000100_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000100_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000100_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000100_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000100_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000100_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000100_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000100_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000100_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000100_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000100_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000100_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000100_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000100_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000100_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000100_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000100_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000100_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000100_url.sedml\ncreate_links: /BIOMD0000000100_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000100_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000100_url.sedml/autogen_plot_for_task1, shape: (6, 1001), type: float64\niterating over chunks for /BIOMD0000000100_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 6, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000100_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000100_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000100_url.sedml/autogen_report_for_task1, shape: (49, 1001), type: float64\niterating over chunks for /BIOMD0000000100_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 49, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000100_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6471084149c0d898ffddb249\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.\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 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":1.392097,"sedDocuments":[{"location":"BIOMD0000000100_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  BIOMD0000000100_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 49 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 5 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000100_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":0.98843,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.15604,"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":0.34221,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_EC","status":"SUCCEEDED"},{"id":"autogen_task1_Z","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_Y","status":"SUCCEEDED"},{"id":"autogen_task1_GP","status":"SUCCEEDED"},{"id":"autogen_task1_v0","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_Vm2","status":"SUCCEEDED"},{"id":"autogen_task1_K2","status":"SUCCEEDED"},{"id":"autogen_task1_Vm3","status":"SUCCEEDED"},{"id":"autogen_task1_m","status":"SUCCEEDED"},{"id":"autogen_task1_Ka","status":"SUCCEEDED"},{"id":"autogen_task1_Ky","status":"SUCCEEDED"},{"id":"autogen_task1_Kz","status":"SUCCEEDED"},{"id":"autogen_task1_Kf","status":"SUCCEEDED"},{"id":"autogen_task1_K","status":"SUCCEEDED"},{"id":"autogen_task1_V4","status":"SUCCEEDED"},{"id":"autogen_task1_Vm5","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_K5","status":"SUCCEEDED"},{"id":"autogen_task1_Kd","status":"SUCCEEDED"},{"id":"autogen_task1_epsilon","status":"SUCCEEDED"},{"id":"autogen_task1_Vpm1","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_Ka5","status":"SUCCEEDED"},{"id":"autogen_task1_K1","status":"SUCCEEDED"},{"id":"autogen_task1_Ka6","status":"SUCCEEDED"},{"id":"autogen_task1_Vpm2","status":"SUCCEEDED"},{"id":"autogen_task1_alpha","status":"SUCCEEDED"},{"id":"autogen_task1_G","status":"SUCCEEDED"},{"id":"autogen_task1_Ka1","status":"SUCCEEDED"},{"id":"autogen_task1_Kp2","status":"SUCCEEDED"},{"id":"autogen_task1_Ka2","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_extracellular","status":"SUCCEEDED"},{"id":"autogen_task1_cytosol","status":"SUCCEEDED"},{"id":"autogen_task1_intravesicular","status":"SUCCEEDED"},{"id":"autogen_task1_vin","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_R3","status":"SUCCEEDED"},{"id":"autogen_task1_Rkf","status":"SUCCEEDED"},{"id":"autogen_task1_Rkz","status":"SUCCEEDED"},{"id":"autogen_task1_R4","status":"SUCCEEDED"},{"id":"autogen_task1_R5","status":"SUCCEEDED"},{"id":"autogen_task1_R6","status":"SUCCEEDED"},{"id":"autogen_task1_R7","status":"SUCCEEDED"},{"id":"autogen_task1_R8","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.341362,"curves":[{"id":"autogen_curve_task1_EC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Z","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Y","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GP","status":"SUCCEEDED"}]}]}]}