{"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    437      0 --:--:-- --:--:-- --:--:--   437\n\r100  486k  100  486k    0     0  1083k      0 --:--:-- --:--:-- --:--:-- 1083k\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 (19.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/rawLog.txt\nCompleted 5.8 KiB/5.8 KiB (58.1 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/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/BIOMD0000000294_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000294_url.sedml/autogen_plot_for_task1.pdf (deflated 25%)\n  adding: outputs/reports.h5 (deflated 7%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/410.5 KiB (5.6 MiB/s) with 1 file(s) remaining\rCompleted 410.5 KiB/410.5 KiB (2.9 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/outputs/reports.h5\nCompleted 9.6 KiB/419.5 KiB (134.4 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/outputs/plots.zip\nCompleted 9.6 KiB/419.5 KiB (134.4 KiB/s) with 3 file(s) remaining\rCompleted 265.6 KiB/419.5 KiB (3.4 MiB/s) with 3 file(s) remaining\rCompleted 268.4 KiB/419.5 KiB (1.7 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/rawLog.txt\nCompleted 268.4 KiB/419.5 KiB (1.7 MiB/s) with 2 file(s) remaining\rCompleted 406.4 KiB/419.5 KiB (2.5 MiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/output.zip\nCompleted 406.4 KiB/419.5 KiB (2.5 MiB/s) with 1 file(s) remaining\rCompleted 419.5 KiB/419.5 KiB (2.5 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000294_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/outputs/BIOMD0000000294_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/BIOMD0000000294-biopax2.owl  \n  inflating: contents/BIOMD0000000294-biopax3.owl  \n  inflating: contents/BIOMD0000000294-matlab.m  \n  inflating: contents/BIOMD0000000294.m  \n  inflating: contents/BIOMD0000000294.ode  \n  inflating: contents/BIOMD0000000294.pdf  \n  inflating: contents/BIOMD0000000294.png  \n  inflating: contents/BIOMD0000000294.svg  \n  inflating: contents/BIOMD0000000294.vcml  \n  inflating: contents/BIOMD0000000294_url.sedml  \n  inflating: contents/BIOMD0000000294_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 27.1 KiB/858.0 KiB (350.4 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000294-biopax2.owl to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294-biopax2.owl\nCompleted 27.1 KiB/858.0 KiB (350.4 KiB/s) with 14 file(s) remaining\rCompleted 35.7 KiB/858.0 KiB (243.9 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000294-matlab.m to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294-matlab.m\nCompleted 35.7 KiB/858.0 KiB (243.9 KiB/s) with 13 file(s) remaining\rCompleted 44.2 KiB/858.0 KiB (284.5 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000294.m to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294.m\nCompleted 44.2 KiB/858.0 KiB (284.5 KiB/s) with 12 file(s) remaining\rCompleted 52.7 KiB/858.0 KiB (323.6 KiB/s) with 12 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/metadata.rdf\nCompleted 52.7 KiB/858.0 KiB (323.6 KiB/s) with 11 file(s) remaining\rCompleted 98.7 KiB/858.0 KiB (598.1 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000294.svg to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294.svg\nCompleted 98.7 KiB/858.0 KiB (598.1 KiB/s) with 10 file(s) remaining\rCompleted 338.6 KiB/858.0 KiB (2.0 MiB/s) with 10 file(s) remaining \rupload: contents/BIOMD0000000294.pdf to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294.pdf\nCompleted 338.6 KiB/858.0 KiB (2.0 MiB/s) with 9 file(s) remaining\rCompleted 403.2 KiB/858.0 KiB (2.3 MiB/s) with 9 file(s) remaining\rupload: contents/BIOMD0000000294.vcml to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294.vcml\nCompleted 403.2 KiB/858.0 KiB (2.3 MiB/s) with 8 file(s) remaining\rCompleted 409.3 KiB/858.0 KiB (2.2 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000294.ode to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294.ode\nCompleted 409.3 KiB/858.0 KiB (2.2 MiB/s) with 7 file(s) remaining\rCompleted 452.6 KiB/858.0 KiB (2.1 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000294-biopax3.owl to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294-biopax3.owl\nCompleted 452.6 KiB/858.0 KiB (2.1 MiB/s) with 6 file(s) remaining\rCompleted 655.8 KiB/858.0 KiB (3.0 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000294.png to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294.png\nCompleted 655.8 KiB/858.0 KiB (3.0 MiB/s) with 5 file(s) remaining\rCompleted 657.6 KiB/858.0 KiB (3.0 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/manifest.xml\nCompleted 657.6 KiB/858.0 KiB (3.0 MiB/s) with 4 file(s) remaining\rCompleted 707.3 KiB/858.0 KiB (2.8 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000294_url.xml to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294_url.xml\nCompleted 707.3 KiB/858.0 KiB (2.8 MiB/s) with 3 file(s) remaining\rCompleted 707.8 KiB/858.0 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/curation_notes.txt\nCompleted 707.8 KiB/858.0 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 739.5 KiB/858.0 KiB (2.8 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000294_url.sedml to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/BIOMD0000000294_url.sedml\nCompleted 739.5 KiB/858.0 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 858.0 KiB/858.0 KiB (3.1 MiB/s) with 1 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/contents/curation_image.png\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 8.7 KiB/8.7 KiB (83.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6488f139ee26f4323c90007c/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000294_url.sedml\ncreating dataset /BIOMD0000000294_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\ndataset created, uuid: d-8a7ca4d4-b6c86ce7-4cb1-a6be38-c464dd, chunk_size: (12, 1001)\ncreating dataset /BIOMD0000000294_url.sedml/autogen_report_for_task1, shape: (61, 1001), type: float64\ndataset created, uuid: d-8a7ca4d4-b6c86ce7-750a-d4912b-ae0a06, chunk_size: (61, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000294_url.sedml\ncreating attribute uri in /BIOMD0000000294_url.sedml\ncreating attribute _type in /BIOMD0000000294_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000294_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000294_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000294_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000294_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000294_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000294_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000294_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000294_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000294_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000294_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000294_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000294_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000294_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000294_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000294_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000294_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000294_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000294_url.sedml\ncreate_links: /BIOMD0000000294_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000294_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000294_url.sedml/autogen_plot_for_task1, shape: (12, 1001), type: float64\niterating over chunks for /BIOMD0000000294_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 12, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000294_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000294_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000294_url.sedml/autogen_report_for_task1, shape: (61, 1001), type: float64\niterating over chunks for /BIOMD0000000294_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 61, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000294_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/6488f139ee26f4323c90007c\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 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 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":2.038053,"sedDocuments":[{"location":"BIOMD0000000294_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  BIOMD0000000294_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 61 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 11 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000294_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":1.461225,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.251837,"algorithm":"KISAO_0000019","simulatorDetails":[{"key":"method","value":"simulate"},{"key":"solver","value":"cvode"},{"key":"relative_tolerance","value":0.000001},{"key":"absolute_tolerance","value":1e-12},{"key":"stiff","value":true},{"key":"maximum_bdf_order","value":5},{"key":"maximum_adams_order","value":12},{"key":"maximum_num_steps","value":20000},{"key":"maximum_time_step","value":0},{"key":"minimum_time_step","value":0},{"key":"initial_time_step","value":0},{"key":"multiple_steps","value":false},{"key":"variable_step_size","value":false},{"key":"max_output_rows","value":100000}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.443007,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_N","status":"SUCCEEDED"},{"id":"autogen_task1_S","status":"SUCCEEDED"},{"id":"autogen_task1_I1","status":"SUCCEEDED"},{"id":"autogen_task1_I2","status":"SUCCEEDED"},{"id":"autogen_task1_R1","status":"SUCCEEDED"},{"id":"autogen_task1_R2","status":"SUCCEEDED"},{"id":"autogen_task1_V","status":"SUCCEEDED"},{"id":"autogen_task1_Iv2","status":"SUCCEEDED"},{"id":"autogen_task1_J2","status":"SUCCEEDED"},{"id":"autogen_task1_J1","status":"SUCCEEDED"},{"id":"autogen_task1_R","status":"SUCCEEDED"},{"id":"autogen_task1_mu","status":"SUCCEEDED"},{"id":"autogen_task1_l_e","status":"SUCCEEDED"},{"id":"autogen_task1_beta","status":"SUCCEEDED"},{"id":"autogen_task1_R0","status":"SUCCEEDED"},{"id":"autogen_task1_gamma","status":"SUCCEEDED"},{"id":"autogen_task1_p","status":"SUCCEEDED"},{"id":"autogen_task1_tau","status":"SUCCEEDED"},{"id":"autogen_task1_theta","status":"SUCCEEDED"},{"id":"autogen_task1_nu","status":"SUCCEEDED"},{"id":"autogen_task1_eta","status":"SUCCEEDED"},{"id":"autogen_task1_sigma","status":"SUCCEEDED"},{"id":"autogen_task1_sigmaV","status":"SUCCEEDED"},{"id":"autogen_task1_tInf","status":"SUCCEEDED"},{"id":"autogen_task1_tImm","status":"SUCCEEDED"},{"id":"autogen_task1_tImm_V","status":"SUCCEEDED"},{"id":"autogen_task1_strain1_frac","status":"SUCCEEDED"},{"id":"autogen_task1_strain2_frac","status":"SUCCEEDED"},{"id":"autogen_task1_S_frac","status":"SUCCEEDED"},{"id":"autogen_task1_V_frac","status":"SUCCEEDED"},{"id":"autogen_task1_R_1_frac","status":"SUCCEEDED"},{"id":"autogen_task1_R_2_frac","status":"SUCCEEDED"},{"id":"autogen_task1_R_frac","status":"SUCCEEDED"},{"id":"autogen_task1_env","status":"SUCCEEDED"},{"id":"autogen_task1_r1","status":"SUCCEEDED"},{"id":"autogen_task1_r2","status":"SUCCEEDED"},{"id":"autogen_task1_r3","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_task1_r9","status":"SUCCEEDED"},{"id":"autogen_task1_r10","status":"SUCCEEDED"},{"id":"autogen_task1_r11","status":"SUCCEEDED"},{"id":"autogen_task1_r12","status":"SUCCEEDED"},{"id":"autogen_task1_r13","status":"SUCCEEDED"},{"id":"autogen_task1_r14","status":"SUCCEEDED"},{"id":"autogen_task1_r15","status":"SUCCEEDED"},{"id":"autogen_task1_r16","status":"SUCCEEDED"},{"id":"autogen_task1_r17","status":"SUCCEEDED"},{"id":"autogen_task1_r18","status":"SUCCEEDED"},{"id":"autogen_task1_r19","status":"SUCCEEDED"},{"id":"autogen_task1_r20","status":"SUCCEEDED"},{"id":"autogen_task1_r21","status":"SUCCEEDED"},{"id":"autogen_task1_r22","status":"SUCCEEDED"},{"id":"autogen_task1_r23","status":"SUCCEEDED"},{"id":"autogen_task1_r24","status":"SUCCEEDED"},{"id":"autogen_task1_r25","status":"SUCCEEDED"},{"id":"autogen_task1_r26","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.589111,"curves":[{"id":"autogen_curve_task1_N","status":"SUCCEEDED"},{"id":"autogen_curve_task1_S","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_V","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Iv2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_J2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_J1","status":"SUCCEEDED"},{"id":"autogen_curve_task1_R","status":"SUCCEEDED"}]}]}]}