{"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    438      0 --:--:-- --:--:-- --:--:--   438\n\r100  271k  100  271k    0     0   590k      0 --:--:-- --:--:-- --:--:--  590k\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 (23.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 5.8 KiB/5.8 KiB (77.5 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 85%)\n  adding: outputs/BIOMD0000000001_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf (deflated 30%)\n  adding: outputs/reports.h5 (deflated 11%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/323.8 KiB (128.9 KiB/s) with 1 file(s) remaining\rCompleted 323.8 KiB/323.8 KiB (154.5 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/319.7 KiB (2.9 MiB/s) with 4 file(s) remaining\rCompleted 266.8 KiB/319.7 KiB (2.1 MiB/s) with 4 file(s) remaining\rupload: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf\nCompleted 266.8 KiB/319.7 KiB (2.1 MiB/s) with 3 file(s) remaining\rCompleted 274.3 KiB/319.7 KiB (2.2 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/outputs/plots.zip\nCompleted 274.3 KiB/319.7 KiB (2.2 MiB/s) with 2 file(s) remaining\rCompleted 277.2 KiB/319.7 KiB (2.0 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/rawLog.txt\nCompleted 277.2 KiB/319.7 KiB (2.0 MiB/s) with 1 file(s) remaining\rCompleted 319.7 KiB/319.7 KiB (1.9 MiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/output.zip\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/BIOMD0000000001-biopax2.owl  \n  inflating: contents/BIOMD0000000001-biopax3.owl  \n  inflating: contents/BIOMD0000000001-matlab.m  \n  inflating: contents/BIOMD0000000001-octave.m  \n  inflating: contents/BIOMD0000000001.m  \n  inflating: contents/BIOMD0000000001.ode  \n  inflating: contents/BIOMD0000000001.pdf  \n  inflating: contents/BIOMD0000000001.png  \n  inflating: contents/BIOMD0000000001.svg  \n  inflating: contents/BIOMD0000000001.vcml  \n  inflating: contents/BIOMD0000000001_url.sedml  \n  inflating: contents/BIOMD0000000001_url.xml  \n  inflating: contents/curation_image.png  \n  inflating: contents/curation_notes.txt  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 23.1 KiB/~592.2 KiB (245.5 KiB/s) with ~14 file(s) remaining (calculating...)\rupload: contents/BIOMD0000000001-biopax2.owl to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001-biopax2.owl\nCompleted 23.1 KiB/~592.2 KiB (245.5 KiB/s) with ~13 file(s) remaining (calculating...)\rCompleted 32.0 KiB/600.6 KiB (263.6 KiB/s) with 15 file(s) remaining                   \rupload: contents/BIOMD0000000001-octave.m to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001-octave.m\nCompleted 32.0 KiB/600.6 KiB (263.6 KiB/s) with 14 file(s) remaining\rCompleted 40.8 KiB/600.6 KiB (310.6 KiB/s) with 14 file(s) remaining\rupload: contents/BIOMD0000000001-matlab.m to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001-matlab.m\nCompleted 40.8 KiB/600.6 KiB (310.6 KiB/s) with 13 file(s) remaining\rCompleted 85.2 KiB/600.6 KiB (530.2 KiB/s) with 13 file(s) remaining\rupload: contents/curation_image.png to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/curation_image.png\nCompleted 85.2 KiB/600.6 KiB (530.2 KiB/s) with 12 file(s) remaining\rCompleted 122.5 KiB/600.6 KiB (665.4 KiB/s) with 12 file(s) remaining\rupload: contents/BIOMD0000000001.svg to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001.svg\nCompleted 122.5 KiB/600.6 KiB (665.4 KiB/s) with 11 file(s) remaining\rCompleted 129.0 KiB/600.6 KiB (682.4 KiB/s) with 11 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/metadata.rdf\nCompleted 129.0 KiB/600.6 KiB (682.4 KiB/s) with 10 file(s) remaining\rCompleted 163.8 KiB/600.6 KiB (771.8 KiB/s) with 10 file(s) remaining\rupload: contents/BIOMD0000000001_url.sedml to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001_url.sedml\nCompleted 163.8 KiB/600.6 KiB (771.8 KiB/s) with 9 file(s) remaining\rCompleted 383.6 KiB/600.6 KiB (1.7 MiB/s) with 9 file(s) remaining  \rupload: contents/BIOMD0000000001.pdf to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001.pdf\nCompleted 383.6 KiB/600.6 KiB (1.7 MiB/s) with 8 file(s) remaining\rCompleted 447.9 KiB/600.6 KiB (2.0 MiB/s) with 8 file(s) remaining\rupload: contents/BIOMD0000000001.vcml to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001.vcml\nCompleted 447.9 KiB/600.6 KiB (2.0 MiB/s) with 7 file(s) remaining\rCompleted 484.7 KiB/600.6 KiB (2.1 MiB/s) with 7 file(s) remaining\rupload: contents/BIOMD0000000001-biopax3.owl to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001-biopax3.owl\nCompleted 484.7 KiB/600.6 KiB (2.1 MiB/s) with 6 file(s) remaining\rCompleted 485.1 KiB/600.6 KiB (2.0 MiB/s) with 6 file(s) remaining\rupload: contents/curation_notes.txt to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/curation_notes.txt\nCompleted 485.1 KiB/600.6 KiB (2.0 MiB/s) with 5 file(s) remaining\rCompleted 486.9 KiB/600.6 KiB (2.0 MiB/s) with 5 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/manifest.xml\nCompleted 486.9 KiB/600.6 KiB (2.0 MiB/s) with 4 file(s) remaining\rCompleted 495.8 KiB/600.6 KiB (2.0 MiB/s) with 4 file(s) remaining\rupload: contents/BIOMD0000000001.m to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001.m\nCompleted 495.8 KiB/600.6 KiB (2.0 MiB/s) with 3 file(s) remaining\rCompleted 501.8 KiB/600.6 KiB (1.9 MiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000001.ode to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001.ode\nCompleted 501.8 KiB/600.6 KiB (1.9 MiB/s) with 2 file(s) remaining\rCompleted 553.3 KiB/600.6 KiB (2.1 MiB/s) with 2 file(s) remaining\rupload: contents/BIOMD0000000001_url.xml to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001_url.xml\nCompleted 553.3 KiB/600.6 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 600.6 KiB/600.6 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000001.png to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/contents/BIOMD0000000001.png\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 9.4 KiB/9.4 KiB (122.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674e9088dc98815570335845/rawLog.txt\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 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 and upload the outputs of the simulation run ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":48.623701,"sedDocuments":[{"location":"BIOMD0000000001_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  BIOMD0000000001_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 66 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 12 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000001_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":47.865271,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":46.490642,"algorithm":"KISAO_0000496","simulatorDetails":[{"key":"solver","value":"amici.amici.CVodeSolver"},{"key":"method","value":"amici.swig_wrappers.runAmiciSimulation"},{"key":"arguments"}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.486483,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_BLL","status":"SUCCEEDED"},{"id":"autogen_task1_IL","status":"SUCCEEDED"},{"id":"autogen_task1_AL","status":"SUCCEEDED"},{"id":"autogen_task1_A","status":"SUCCEEDED"},{"id":"autogen_task1_BL","status":"SUCCEEDED"},{"id":"autogen_task1_B","status":"SUCCEEDED"},{"id":"autogen_task1_DLL","status":"SUCCEEDED"},{"id":"autogen_task1_D","status":"SUCCEEDED"},{"id":"autogen_task1_ILL","status":"SUCCEEDED"},{"id":"autogen_task1_DL","status":"SUCCEEDED"},{"id":"autogen_task1_I","status":"SUCCEEDED"},{"id":"autogen_task1_ALL","status":"SUCCEEDED"},{"id":"autogen_task1_kf_0","status":"SUCCEEDED"},{"id":"autogen_task1_kr_0","status":"SUCCEEDED"},{"id":"autogen_task1_kf_1","status":"SUCCEEDED"},{"id":"autogen_task1_kr_1","status":"SUCCEEDED"},{"id":"autogen_task1_kf_2","status":"SUCCEEDED"},{"id":"autogen_task1_kr_2","status":"SUCCEEDED"},{"id":"autogen_task1_kf_3","status":"SUCCEEDED"},{"id":"autogen_task1_kr_3","status":"SUCCEEDED"},{"id":"autogen_task1_kf_4","status":"SUCCEEDED"},{"id":"autogen_task1_kr_4","status":"SUCCEEDED"},{"id":"autogen_task1_kf_5","status":"SUCCEEDED"},{"id":"autogen_task1_kr_5","status":"SUCCEEDED"},{"id":"autogen_task1_kf_6","status":"SUCCEEDED"},{"id":"autogen_task1_kr_6","status":"SUCCEEDED"},{"id":"autogen_task1_kf_7","status":"SUCCEEDED"},{"id":"autogen_task1_kr_7","status":"SUCCEEDED"},{"id":"autogen_task1_kf_8","status":"SUCCEEDED"},{"id":"autogen_task1_kr_8","status":"SUCCEEDED"},{"id":"autogen_task1_kf_9","status":"SUCCEEDED"},{"id":"autogen_task1_kr_9","status":"SUCCEEDED"},{"id":"autogen_task1_kf_10","status":"SUCCEEDED"},{"id":"autogen_task1_kr_10","status":"SUCCEEDED"},{"id":"autogen_task1_kf_11","status":"SUCCEEDED"},{"id":"autogen_task1_kr_11","status":"SUCCEEDED"},{"id":"autogen_task1_kf_12","status":"SUCCEEDED"},{"id":"autogen_task1_kr_12","status":"SUCCEEDED"},{"id":"autogen_task1_kf_13","status":"SUCCEEDED"},{"id":"autogen_task1_kr_13","status":"SUCCEEDED"},{"id":"autogen_task1_kf_14","status":"SUCCEEDED"},{"id":"autogen_task1_kr_14","status":"SUCCEEDED"},{"id":"autogen_task1_kf_15","status":"SUCCEEDED"},{"id":"autogen_task1_kr_15","status":"SUCCEEDED"},{"id":"autogen_task1_kf_16","status":"SUCCEEDED"},{"id":"autogen_task1_kr_16","status":"SUCCEEDED"},{"id":"autogen_task1_t2","status":"SUCCEEDED"},{"id":"autogen_task1_comp1","status":"SUCCEEDED"},{"id":"autogen_task1_React0","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_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.676395,"curves":[{"id":"autogen_curve_task1_BLL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_A","status":"SUCCEEDED"},{"id":"autogen_curve_task1_BL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_B","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DLL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_D","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ILL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DL","status":"SUCCEEDED"},{"id":"autogen_curve_task1_I","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ALL","status":"SUCCEEDED"}]}]}]}