{"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    451      0 --:--:-- --:--:-- --:--:--   449\n\r100  236k  100  236k    0     0   544k      0 --:--:-- --:--:-- --:--:--  544k\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 (22.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/rawLog.txt\nCompleted 4.3 KiB/4.3 KiB (62.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 82%)\n  adding: outputs/BIOMD0000000423_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000423_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\nsrun: Job 6630911 step creation temporarily disabled, retrying\nsrun: Step created for job 6630911\nCompleted 256.0 KiB/256.7 KiB (5.3 MiB/s) with 1 file(s) remaining\rCompleted 256.7 KiB/256.7 KiB (2.3 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/outputs/reports.h5\nCompleted 240.4 KiB/263.8 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/output.zip\nCompleted 240.4 KiB/263.8 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 243.3 KiB/263.8 KiB (2.0 MiB/s) with 3 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/rawLog.txt\nCompleted 243.3 KiB/263.8 KiB (2.0 MiB/s) with 2 file(s) remaining\rCompleted 252.0 KiB/263.8 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/outputs/plots.zip\nCompleted 252.0 KiB/263.8 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 263.8 KiB/263.8 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: outputs/BIOMD0000000423_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/outputs/BIOMD0000000423_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/BIOMD0000000423-biopax2.owl  \n  inflating: contents/BIOMD0000000423-biopax3.owl  \n  inflating: contents/BIOMD0000000423-matlab.m  \n  inflating: contents/BIOMD0000000423-octave.m  \n  inflating: contents/BIOMD0000000423.m  \n  inflating: contents/BIOMD0000000423.ode  \n  inflating: contents/BIOMD0000000423.pdf  \n  inflating: contents/BIOMD0000000423.png  \n  inflating: contents/BIOMD0000000423.sci  \n  inflating: contents/BIOMD0000000423.svg  \n  inflating: contents/BIOMD0000000423.vcml  \n  inflating: contents/BIOMD0000000423_url.sedml  \n  inflating: contents/BIOMD0000000423_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 16.9 KiB/~441.2 KiB (245.1 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000423-biopax2.owl to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423-biopax2.owl\nCompleted 16.9 KiB/~441.2 KiB (245.1 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 22.9 KiB/447.9 KiB (184.5 KiB/s) with 16 file(s) remaining                   \rupload: contents/BIOMD0000000423-matlab.m to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423-matlab.m\nCompleted 22.9 KiB/447.9 KiB (184.5 KiB/s) with 15 file(s) remaining\rCompleted 26.3 KiB/447.9 KiB (208.7 KiB/s) with 15 file(s) remaining\rupload: contents/BIOMD0000000423.sci to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423.sci\nCompleted 26.3 KiB/447.9 KiB (208.7 KiB/s) with 14 file(s) remaining\rCompleted 49.3 KiB/447.9 KiB (387.1 KiB/s) with 14 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/curation_image.png\nCompleted 49.3 KiB/447.9 KiB (387.1 KiB/s) with 13 file(s) remaining\rCompleted 55.3 KiB/447.9 KiB (428.9 KiB/s) with 13 file(s) remaining\rupload: contents/BIOMD0000000423-octave.m to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423-octave.m\nCompleted 55.3 KiB/447.9 KiB (428.9 KiB/s) with 12 file(s) remaining\rCompleted 121.7 KiB/447.9 KiB (861.2 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000423.png to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423.png\nCompleted 121.7 KiB/447.9 KiB (861.2 KiB/s) with 11 file(s) remaining\rCompleted 145.6 KiB/447.9 KiB (946.4 KiB/s) with 11 file(s) remaining\rupload: contents/BIOMD0000000423.svg to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423.svg\nCompleted 145.6 KiB/447.9 KiB (946.4 KiB/s) with 10 file(s) remaining\rCompleted 167.7 KiB/447.9 KiB (932.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000423_url.sedml to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423_url.sedml\nCompleted 167.7 KiB/447.9 KiB (932.8 KiB/s) with 9 file(s) remaining\rCompleted 201.2 KiB/447.9 KiB (1.1 MiB/s) with 9 file(s) remaining  \rupload: contents/BIOMD0000000423.vcml to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423.vcml\nCompleted 201.2 KiB/447.9 KiB (1.1 MiB/s) with 8 file(s) remaining\rCompleted 203.2 KiB/447.9 KiB (1.0 MiB/s) with 8 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/manifest.xml\nCompleted 203.2 KiB/447.9 KiB (1.0 MiB/s) with 7 file(s) remaining\rCompleted 207.5 KiB/447.9 KiB (1.0 MiB/s) with 7 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/metadata.rdf\nCompleted 207.5 KiB/447.9 KiB (1.0 MiB/s) with 6 file(s) remaining\rCompleted 229.1 KiB/447.9 KiB (1.1 MiB/s) with 6 file(s) remaining\rupload: contents/BIOMD0000000423_url.xml to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423_url.xml\nCompleted 229.1 KiB/447.9 KiB (1.1 MiB/s) with 5 file(s) remaining\rCompleted 235.0 KiB/447.9 KiB (1.1 MiB/s) with 5 file(s) remaining\rupload: contents/BIOMD0000000423.m to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423.m\nCompleted 235.0 KiB/447.9 KiB (1.1 MiB/s) with 4 file(s) remaining\rCompleted 235.5 KiB/447.9 KiB (1.1 MiB/s) with 4 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/curation_notes.txt\nCompleted 235.5 KiB/447.9 KiB (1.1 MiB/s) with 3 file(s) remaining\rCompleted 261.6 KiB/447.9 KiB (1.2 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000423-biopax3.owl to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423-biopax3.owl\nCompleted 261.6 KiB/447.9 KiB (1.2 MiB/s) with 2 file(s) remaining\rCompleted 265.5 KiB/447.9 KiB (1.1 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000423.ode to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423.ode\nCompleted 265.5 KiB/447.9 KiB (1.1 MiB/s) with 1 file(s) remaining\rCompleted 447.9 KiB/447.9 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000423.pdf to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/contents/BIOMD0000000423.pdf\n\n\u001b[0;36m==================================================== Updating log ===================================================\u001b[0m\nCompleted 9.4 KiB/9.4 KiB (119.9 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/647a4b280fb37cdb9ae731f3/rawLog.txt\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000423_url.sedml\ncreating dataset /BIOMD0000000423_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\ndataset created, uuid: d-e0cc27ae-5f6a6770-be35-552779-13eecf, chunk_size: (10, 1001)\ncreating dataset /BIOMD0000000423_url.sedml/autogen_report_for_task1, shape: (41, 1001), type: float64\ndataset created, uuid: d-e0cc27ae-5f6a6770-6e3a-c596d6-59fd19, chunk_size: (41, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000423_url.sedml\ncreating attribute uri in /BIOMD0000000423_url.sedml\ncreating attribute _type in /BIOMD0000000423_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000423_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000423_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000423_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000423_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000423_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlId in /BIOMD0000000423_url.sedml/autogen_plot_for_task1\ncreating attribute sedmlName in /BIOMD0000000423_url.sedml/autogen_plot_for_task1\ncreating attribute uri in /BIOMD0000000423_url.sedml/autogen_plot_for_task1\ncreating attribute _type in /BIOMD0000000423_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000423_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetIds in /BIOMD0000000423_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetLabels in /BIOMD0000000423_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetNames in /BIOMD0000000423_url.sedml/autogen_report_for_task1\ncreating attribute sedmlDataSetShapes in /BIOMD0000000423_url.sedml/autogen_report_for_task1\ncreating attribute sedmlId in /BIOMD0000000423_url.sedml/autogen_report_for_task1\ncreating attribute sedmlName in /BIOMD0000000423_url.sedml/autogen_report_for_task1\ncreating attribute uri in /BIOMD0000000423_url.sedml/autogen_report_for_task1\ncreate_links: /\ngot link: BIOMD0000000423_url.sedml\ncreate_links: /BIOMD0000000423_url.sedml\ngot link: autogen_plot_for_task1\ngot link: autogen_report_for_task1\nwrite_dataset src: /BIOMD0000000423_url.sedml/autogen_plot_for_task1 to tgt: /BIOMD0000000423_url.sedml/autogen_plot_for_task1, shape: (10, 1001), type: float64\niterating over chunks for /BIOMD0000000423_url.sedml/autogen_plot_for_task1\nwriting dataset data for slice: (slice(0, 10, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000423_url.sedml/autogen_plot_for_task1\nwrite_dataset src: /BIOMD0000000423_url.sedml/autogen_report_for_task1 to tgt: /BIOMD0000000423_url.sedml/autogen_report_for_task1, shape: (41, 1001), type: float64\niterating over chunks for /BIOMD0000000423_url.sedml/autogen_report_for_task1\nwriting dataset data for slice: (slice(0, 41, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000423_url.sedml/autogen_report_for_task1\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/647a4b280fb37cdb9ae731f3\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 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.\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":18.974976,"sedDocuments":[{"location":"BIOMD0000000423_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  BIOMD0000000423_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 41 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 9 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000423_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":18.639763,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":17.862688,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.314067,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_IR","status":"SUCCEEDED"},{"id":"autogen_task1_IRins","status":"SUCCEEDED"},{"id":"autogen_task1_IRp","status":"SUCCEEDED"},{"id":"autogen_task1_IRiP","status":"SUCCEEDED"},{"id":"autogen_task1_IRi","status":"SUCCEEDED"},{"id":"autogen_task1_IRS","status":"SUCCEEDED"},{"id":"autogen_task1_IRSiP","status":"SUCCEEDED"},{"id":"autogen_task1_X","status":"SUCCEEDED"},{"id":"autogen_task1_Xp","status":"SUCCEEDED"},{"id":"autogen_task1_k1a","status":"SUCCEEDED"},{"id":"autogen_task1_k1aBasic","status":"SUCCEEDED"},{"id":"autogen_task1_k1b","status":"SUCCEEDED"},{"id":"autogen_task1_k1c","status":"SUCCEEDED"},{"id":"autogen_task1_k1d","status":"SUCCEEDED"},{"id":"autogen_task1_k1e","status":"SUCCEEDED"},{"id":"autogen_task1_k1f","status":"SUCCEEDED"},{"id":"autogen_task1_k1g","status":"SUCCEEDED"},{"id":"autogen_task1_k1r","status":"SUCCEEDED"},{"id":"autogen_task1_k21","status":"SUCCEEDED"},{"id":"autogen_task1_k22","status":"SUCCEEDED"},{"id":"autogen_task1_km2","status":"SUCCEEDED"},{"id":"autogen_task1_km23","status":"SUCCEEDED"},{"id":"autogen_task1_k3","status":"SUCCEEDED"},{"id":"autogen_task1_km3","status":"SUCCEEDED"},{"id":"autogen_task1_ins","status":"SUCCEEDED"},{"id":"autogen_task1_measIRS1","status":"SUCCEEDED"},{"id":"autogen_task1_measIRp","status":"SUCCEEDED"},{"id":"autogen_task1_IRmem","status":"SUCCEEDED"},{"id":"autogen_task1_default","status":"SUCCEEDED"},{"id":"autogen_task1_v1a","status":"SUCCEEDED"},{"id":"autogen_task1_v1b","status":"SUCCEEDED"},{"id":"autogen_task1_v1c","status":"SUCCEEDED"},{"id":"autogen_task1_v1d","status":"SUCCEEDED"},{"id":"autogen_task1_v1e","status":"SUCCEEDED"},{"id":"autogen_task1_v1g","status":"SUCCEEDED"},{"id":"autogen_task1_v1r","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_vm2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_vm3","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.321297,"curves":[{"id":"autogen_curve_task1_IR","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IRins","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IRp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IRiP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IRi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IRS","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IRSiP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_X","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Xp","status":"SUCCEEDED"}]}]}]}