{"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    444      0 --:--:-- --:--:-- --:--:--   445\n\r100  8231  100  8231    0     0  18707      0 --:--:-- --:--:-- --:--:-- 18707\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 (18.0 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 6.2 KiB/6.2 KiB (73.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/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 10%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/349.9 KiB (2.8 MiB/s) with 1 file(s) remaining\rCompleted 349.9 KiB/349.9 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/346.0 KiB (7.9 MiB/s) with 4 file(s) remaining\rCompleted 263.4 KiB/346.0 KiB (2.4 MiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/outputs/plots.zip\nCompleted 263.4 KiB/346.0 KiB (2.4 MiB/s) with 3 file(s) remaining\rCompleted 332.2 KiB/346.0 KiB (2.9 MiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/output.zip\nCompleted 332.2 KiB/346.0 KiB (2.9 MiB/s) with 2 file(s) remaining\rCompleted 343.1 KiB/346.0 KiB (2.9 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf\nCompleted 343.1 KiB/346.0 KiB (2.9 MiB/s) with 1 file(s) remaining\rCompleted 346.0 KiB/346.0 KiB (2.1 MiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/rawLog.txt\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/manifest.xml   \n  inflating: contents/BIOMD0000000001_url.sedml  \n  inflating: contents/BIOMD0000000001_url.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 49.2 KiB/85.3 KiB (516.7 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000001_url.xml to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/contents/BIOMD0000000001_url.xml\nCompleted 49.2 KiB/85.3 KiB (516.7 KiB/s) with 2 file(s) remaining\rCompleted 49.9 KiB/85.3 KiB (451.4 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/contents/manifest.xml\nCompleted 49.9 KiB/85.3 KiB (451.4 KiB/s) with 1 file(s) remaining\rCompleted 85.3 KiB/85.3 KiB (696.9 KiB/s) with 1 file(s) remaining\rupload: contents/BIOMD0000000001_url.sedml to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/contents/BIOMD0000000001_url.sedml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.2 KiB/5.2 KiB (62.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc4c010bb4455d618748a/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 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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[1;33mProcess the metadata in the COMBINE archive ... failed due to: The metadata of the file could not be found:\nThere was an error in processing the metadata file. More information is available at https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/. A validation tool is available at https://run.biosimulations.org/utils/validate-metadata.\nPost the metadata to the API ... failed due to: Metadata not found due to a dependent step failing.\u001b[0m\n\u001b[0;31mPost the SED-ML file to the API ... failed due to: Failed to post SED-ML specs:\nThere was an error uploading the SED-ML specifications to the API.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":2.16265,"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":1.573024,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.30838,"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":0.430861,"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":0.633544,"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"}]}]}]}