{"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    448      0 --:--:-- --:--:-- --:--:--   449\n\r100  220k  100  220k    0     0   507k      0 --:--:-- --:--:-- --:--:--  507k\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 (26.8 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/rawLog.txt\nCompleted 4.4 KiB/4.4 KiB (65.7 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/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/BIOMD0000000179_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000179_url.sedml/autogen_plot_for_task1.pdf (deflated 26%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 248.3 KiB/248.3 KiB (2.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/outputs/reports.h5\nCompleted 2.6 KiB/254.0 KiB (24.6 KiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/rawLog.txt\nCompleted 2.6 KiB/254.0 KiB (24.6 KiB/s) with 3 file(s) remaining\rCompleted 234.1 KiB/254.0 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/output.zip\nCompleted 234.1 KiB/254.0 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 242.4 KiB/254.0 KiB (1.4 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/outputs/plots.zip\nCompleted 242.4 KiB/254.0 KiB (1.4 MiB/s) with 1 file(s) remaining\rCompleted 254.0 KiB/254.0 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000179_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/outputs/BIOMD0000000179_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/BIOMD0000000179-biopax2.owl  \n  inflating: contents/BIOMD0000000179-biopax3.owl  \n  inflating: contents/BIOMD0000000179-matlab.m  \n  inflating: contents/BIOMD0000000179-octave.m  \n  inflating: contents/BIOMD0000000179.m  \n  inflating: contents/BIOMD0000000179.pdf  \n  inflating: contents/BIOMD0000000179.png  \n  inflating: contents/BIOMD0000000179.svg  \n  inflating: contents/BIOMD0000000179.vcml  \n  inflating: contents/BIOMD0000000179_url.sedml  \n  inflating: contents/BIOMD0000000179_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 25.5 KiB/447.8 KiB (347.0 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000179-biopax3.owl to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179-biopax3.owl\nCompleted 25.5 KiB/447.8 KiB (347.0 KiB/s) with 14 file(s) remaining\rCompleted 31.2 KiB/447.8 KiB (322.1 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000179-matlab.m to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179-matlab.m\nCompleted 31.2 KiB/447.8 KiB (322.1 KiB/s) with 13 file(s) remaining\rCompleted 48.7 KiB/447.8 KiB (409.3 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000179-biopax2.owl to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179-biopax2.owl\nCompleted 48.7 KiB/447.8 KiB (409.3 KiB/s) with 12 file(s) remaining\rCompleted 50.5 KiB/447.8 KiB (405.1 KiB/s) with 12 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/manifest.xml\nCompleted 50.5 KiB/447.8 KiB (405.1 KiB/s) with 11 file(s) remaining\rCompleted 56.2 KiB/447.8 KiB (438.9 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000179-octave.m to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179-octave.m\nCompleted 56.2 KiB/447.8 KiB (438.9 KiB/s) with 10 file(s) remaining\rCompleted 80.1 KiB/447.8 KiB (579.5 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000179_url.sedml to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179_url.sedml\nCompleted 80.1 KiB/447.8 KiB (579.5 KiB/s) with 9 file(s) remaining\rCompleted 119.0 KiB/447.8 KiB (855.2 KiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000179.vcml to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179.vcml\nCompleted 119.0 KiB/447.8 KiB (855.2 KiB/s) with 8 file(s) remaining\rCompleted 148.4 KiB/447.8 KiB (991.3 KiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000179_url.xml to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179_url.xml\nCompleted 148.4 KiB/447.8 KiB (991.3 KiB/s) with 7 file(s) remaining\rCompleted 207.5 KiB/447.8 KiB (1.2 MiB/s) with 7 file(s) remaining  \rupload: contents/BIOMD0000000179.png to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179.png\nCompleted 207.5 KiB/447.8 KiB (1.2 MiB/s) with 6 file(s) remaining\rCompleted 213.2 KiB/447.8 KiB (1.1 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000179.m to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179.m\nCompleted 213.2 KiB/447.8 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 213.3 KiB/447.8 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/curation_notes.txt\nCompleted 213.3 KiB/447.8 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 398.6 KiB/447.8 KiB (1.9 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000179.pdf to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179.pdf\nCompleted 398.6 KiB/447.8 KiB (1.9 MiB/s) with 3 file(s) remaining\rCompleted 428.1 KiB/447.8 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000179.svg to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/BIOMD0000000179.svg\nCompleted 428.1 KiB/447.8 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 432.2 KiB/447.8 KiB (1.9 MiB/s) with 2 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/metadata.rdf\nCompleted 432.2 KiB/447.8 KiB (1.9 MiB/s) with 1 file(s) remaining\rCompleted 447.8 KiB/447.8 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.jpeg to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/contents/curation_image.jpeg\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.5 KiB/8.5 KiB (121.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647109419a62a8be53f778e7/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000179_url.sedml\ncreating dataset /BIOMD0000000179_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\ndataset created, uuid: d-7b36a916-478f39eb-c971-66fc99-cbb36c, chunk_size: (8, 1001)\ncreating dataset /BIOMD0000000179_url.sedml/autogen_report_for_task1, shape: (44, 1001), type: float64\ndataset created, uuid: d-7b36a916-478f39eb-0ba8-17ea24-fb604a, chunk_size: (44, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000179_url.sedml\ncreating attribute uri in /BIOMD0000000179_url.sedml\ncreating attribute _type in /BIOMD0000000179_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000179_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000179_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000179_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000179_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000179_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000179_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000179_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000179_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000179_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000179_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000179_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000179_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000179_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000179_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000179_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000179_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000179_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000179_url.sedml\ncreate_links: /BIOMD0000000179_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000179_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000179_url.sedml/autogen_plot_for_task1, shape: (8, 1001), type: float64\niterating over chunks for /BIOMD0000000179_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 8, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000179_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000179_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000179_url.sedml/autogen_report_for_task1, shape: (44, 1001), type: float64\niterating over chunks for /BIOMD0000000179_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 44, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000179_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647109419a62a8be53f778e7\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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":1.427466,"sedDocuments":[{"location":"BIOMD0000000179_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  BIOMD0000000179_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 44 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 7 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000179_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":1.034892,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.161007,"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":0.31911,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_P1","status":"SUCCEEDED"},{"id":"autogen_task1_P1_prime","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_P2","status":"SUCCEEDED"},{"id":"autogen_task1_P2_prime","status":"SUCCEEDED"},{"id":"autogen_task1_P3_prime","status":"SUCCEEDED"},{"id":"autogen_task1_i1","status":"SUCCEEDED"},{"id":"autogen_task1_d_R1","status":"SUCCEEDED"},{"id":"autogen_task1_sP1R1","status":"SUCCEEDED"},{"id":"autogen_task1_d_P1","status":"SUCCEEDED"},{"id":"autogen_task1_sP1_prime_P1","status":"SUCCEEDED"},{"id":"autogen_task1_s1","status":"SUCCEEDED"},{"id":"autogen_task1_n","status":"SUCCEEDED"},{"id":"autogen_task1_s3","status":"SUCCEEDED"},{"id":"autogen_task1_d_P1_prime","status":"SUCCEEDED"},{"id":"autogen_task1_i2","status":"SUCCEEDED"},{"id":"autogen_task1_d_R2","status":"SUCCEEDED"},{"id":"autogen_task1_sP2R2","status":"SUCCEEDED"},{"id":"autogen_task1_d_P2","status":"SUCCEEDED"},{"id":"autogen_task1_sP2_prime_P2","status":"SUCCEEDED"},{"id":"autogen_task1_s2","status":"SUCCEEDED"},{"id":"autogen_task1_d_P2_prime","status":"SUCCEEDED"},{"id":"autogen_task1_sP3_prime_P2_prime","status":"SUCCEEDED"},{"id":"autogen_task1_d_P3_prime","status":"SUCCEEDED"},{"id":"autogen_task1_compartment","status":"SUCCEEDED"},{"id":"autogen_task1_React1","status":"SUCCEEDED"},{"id":"autogen_task1_React2","status":"SUCCEEDED"},{"id":"autogen_task1_React3","status":"SUCCEEDED"},{"id":"autogen_task1_React4","status":"SUCCEEDED"},{"id":"autogen_task1_React5","status":"SUCCEEDED"},{"id":"autogen_task1_React6","status":"SUCCEEDED"},{"id":"autogen_task1_React7","status":"SUCCEEDED"},{"id":"autogen_task1_React8","status":"SUCCEEDED"},{"id":"autogen_task1_React9","status":"SUCCEEDED"},{"id":"autogen_task1_React10","status":"SUCCEEDED"},{"id":"autogen_task1_React11","status":"SUCCEEDED"},{"id":"autogen_task1_React12","status":"SUCCEEDED"},{"id":"autogen_task1_React13","status":"SUCCEEDED"},{"id":"autogen_task1_React14","status":"SUCCEEDED"},{"id":"autogen_task1_React15","status":"SUCCEEDED"},{"id":"autogen_task1_React16","status":"SUCCEEDED"},{"id":"autogen_task1_React17","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.406335,"curves":[{"id":"autogen_curve_task1_R1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P1_prime","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P2_prime","status":"SUCCEEDED"},{"id":"autogen_curve_task1_P3_prime","status":"SUCCEEDED"}]}]}]}