{"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    465      0 --:--:-- --:--:-- --:--:--   466\n\r100 20725  100 20725    0     0  49960      0 --:--:-- --:--:-- --:--:-- 49960\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/6752df579fa297efdca19fe9/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 10.7 KiB/10.7 KiB (138.0 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6752df579fa297efdca19fe9/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 89%)\n  adding: outputs/BIOMD0000000239_url.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000239_url.sedml/autogen_plot_for_task1.pdf (deflated 23%)\n  adding: outputs/reports.h5 (deflated 4%)\n  adding: rawLog.txt (deflated 71%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/1.2 MiB (3.5 MiB/s) with 1 file(s) remaining\rCompleted 512.0 KiB/1.2 MiB (4.5 MiB/s) with 1 file(s) remaining\rCompleted 768.0 KiB/1.2 MiB (5.5 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/1.2 MiB (6.3 MiB/s) with 1 file(s) remaining  \rCompleted 1.2 MiB/1.2 MiB (4.9 MiB/s) with 1 file(s) remaining  \rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6752df579fa297efdca19fe9/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 3.1 KiB/1.2 MiB (34.9 KiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6752df579fa297efdca19fe9/rawLog.txt\nCompleted 3.1 KiB/1.2 MiB (34.9 KiB/s) with 3 file(s) remaining\rCompleted 259.1 KiB/1.2 MiB (2.8 MiB/s) with 3 file(s) remaining\rCompleted 515.1 KiB/1.2 MiB (4.0 MiB/s) with 3 file(s) remaining\rCompleted 532.0 KiB/1.2 MiB (4.0 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6752df579fa297efdca19fe9/outputs/plots.zip\nCompleted 532.0 KiB/1.2 MiB (4.0 MiB/s) with 2 file(s) remaining\rCompleted 554.5 KiB/1.2 MiB (4.0 MiB/s) with 2 file(s) remaining\rupload: outputs/BIOMD0000000239_url.sedml/autogen_plot_for_task1.pdf to s3://files.biosimulations.org/simulations/6752df579fa297efdca19fe9/outputs/BIOMD0000000239_url.sedml/autogen_plot_for_task1.pdf\nCompleted 554.5 KiB/1.2 MiB (4.0 MiB/s) with 1 file(s) remaining\rCompleted 810.5 KiB/1.2 MiB (5.3 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/1.2 MiB (6.1 MiB/s) with 1 file(s) remaining  \rCompleted 1.2 MiB/1.2 MiB (4.8 MiB/s) with 1 file(s) remaining  \rupload: ./output.zip to s3://files.biosimulations.org/simulations/6752df579fa297efdca19fe9/output.zip\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/manifest.xml   \n  inflating: contents/BIOMD0000000239_url.sedml  \n  inflating: contents/BIOMD0000000239_url.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 64.2 KiB/304.8 KiB (578.3 KiB/s) with 3 file(s) remaining\rupload: contents/BIOMD0000000239_url.sedml to s3://files.biosimulations.org/simulations/6752df579fa297efdca19fe9/contents/BIOMD0000000239_url.sedml\nCompleted 64.2 KiB/304.8 KiB (578.3 KiB/s) with 2 file(s) remaining\rCompleted 304.1 KiB/304.8 KiB (2.1 MiB/s) with 2 file(s) remaining \rupload: contents/BIOMD0000000239_url.xml to s3://files.biosimulations.org/simulations/6752df579fa297efdca19fe9/contents/BIOMD0000000239_url.xml\nCompleted 304.1 KiB/304.8 KiB (2.1 MiB/s) with 1 file(s) remaining\rCompleted 304.8 KiB/304.8 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6752df579fa297efdca19fe9/contents/manifest.xml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.6 KiB/5.6 KiB (67.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6752df579fa297efdca19fe9/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 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.\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;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":3.350161,"sedDocuments":[{"location":"BIOMD0000000239_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  BIOMD0000000239_url.sedml:\r\n    Tasks (1):\r\n      task1\r\n    Reports (1):\r\n      autogen_report_for_task1: 110 data sets\r\n    Plots (1):\r\n      autogen_plot_for_task1: 59 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000239_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 ...woohoo!\r\n \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":2.818699,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.775723,"algorithm":"KISAO_0000560","simulatorDetails":[{"key":"methodName","value":"lsoda"},{"key":"parameters","value":null}]}],"outputs":[{"id":"autogen_report_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.546457,"dataSets":[{"id":"autogen_time_for_task1","status":"SUCCEEDED"},{"id":"autogen_task1_GLC","status":"SUCCEEDED"},{"id":"autogen_task1_F6P","status":"SUCCEEDED"},{"id":"autogen_task1_FBP","status":"SUCCEEDED"},{"id":"autogen_task1_GAP","status":"SUCCEEDED"},{"id":"autogen_task1_DPG","status":"SUCCEEDED"},{"id":"autogen_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_task1_PYR_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_task1_LAC","status":"SUCCEEDED"},{"id":"autogen_task1_G3P","status":"SUCCEEDED"},{"id":"autogen_task1_DHAP","status":"SUCCEEDED"},{"id":"autogen_task1_OXA_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_Asp_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_Glu_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_OG_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_Mal_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_Acetyl_CoA_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_CoA_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_IsoCitcyt","status":"SUCCEEDED"},{"id":"autogen_task1_Cit_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_ATP_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_ADP_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_task1_NADH_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_NADP_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_NADPH_cyt","status":"SUCCEEDED"},{"id":"autogen_task1_Pyr","status":"SUCCEEDED"},{"id":"autogen_task1_CO2","status":"SUCCEEDED"},{"id":"autogen_task1_CoA","status":"SUCCEEDED"},{"id":"autogen_task1_Acetyl_CoA","status":"SUCCEEDED"},{"id":"autogen_task1_Pi","status":"SUCCEEDED"},{"id":"autogen_task1_Fum","status":"SUCCEEDED"},{"id":"autogen_task1_SCoA","status":"SUCCEEDED"},{"id":"autogen_task1_Suc","status":"SUCCEEDED"},{"id":"autogen_task1_GTP","status":"SUCCEEDED"},{"id":"autogen_task1_GDP","status":"SUCCEEDED"},{"id":"autogen_task1_Ala","status":"SUCCEEDED"},{"id":"autogen_task1_Asp","status":"SUCCEEDED"},{"id":"autogen_task1_Glu","status":"SUCCEEDED"},{"id":"autogen_task1_H2O","status":"SUCCEEDED"},{"id":"autogen_task1_ETFred","status":"SUCCEEDED"},{"id":"autogen_task1_ETFox","status":"SUCCEEDED"},{"id":"autogen_task1_FADH2","status":"SUCCEEDED"},{"id":"autogen_task1_FAD","status":"SUCCEEDED"},{"id":"autogen_task1_OG","status":"SUCCEEDED"},{"id":"autogen_task1_Mal","status":"SUCCEEDED"},{"id":"autogen_task1_OXA","status":"SUCCEEDED"},{"id":"autogen_task1_Cit","status":"SUCCEEDED"},{"id":"autogen_task1_IsoCit","status":"SUCCEEDED"},{"id":"autogen_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_task1_NADP_p","status":"SUCCEEDED"},{"id":"autogen_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_task1_NAD_p","status":"SUCCEEDED"},{"id":"autogen_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_task1_Q","status":"SUCCEEDED"},{"id":"autogen_task1_QH2","status":"SUCCEEDED"},{"id":"autogen_task1_Cytc3p","status":"SUCCEEDED"},{"id":"autogen_task1_Cytc2p","status":"SUCCEEDED"},{"id":"autogen_task1_flow","status":"SUCCEEDED"},{"id":"autogen_task1_CYTOPLASM","status":"SUCCEEDED"},{"id":"autogen_task1_MT_IMS","status":"SUCCEEDED"},{"id":"autogen_task1_MT_IM","status":"SUCCEEDED"},{"id":"autogen_task1_MATRIX","status":"SUCCEEDED"},{"id":"autogen_task1_GLCflow","status":"SUCCEEDED"},{"id":"autogen_task1_LACflow","status":"SUCCEEDED"},{"id":"autogen_task1_GAPflow","status":"SUCCEEDED"},{"id":"autogen_task1_v1","status":"SUCCEEDED"},{"id":"autogen_task1_v2","status":"SUCCEEDED"},{"id":"autogen_task1_v3","status":"SUCCEEDED"},{"id":"autogen_task1_v4","status":"SUCCEEDED"},{"id":"autogen_task1_v5","status":"SUCCEEDED"},{"id":"autogen_task1_v6","status":"SUCCEEDED"},{"id":"autogen_task1_v7","status":"SUCCEEDED"},{"id":"autogen_task1_hidden_1","status":"SUCCEEDED"},{"id":"autogen_task1_v8","status":"SUCCEEDED"},{"id":"autogen_task1_v9","status":"SUCCEEDED"},{"id":"autogen_task1_v10","status":"SUCCEEDED"},{"id":"autogen_task1_v11","status":"SUCCEEDED"},{"id":"autogen_task1_v12","status":"SUCCEEDED"},{"id":"autogen_task1_v14","status":"SUCCEEDED"},{"id":"autogen_task1_v15","status":"SUCCEEDED"},{"id":"autogen_task1_v16","status":"SUCCEEDED"},{"id":"autogen_task1_v17","status":"SUCCEEDED"},{"id":"autogen_task1_v18","status":"SUCCEEDED"},{"id":"autogen_task1_v20","status":"SUCCEEDED"},{"id":"autogen_task1_v21","status":"SUCCEEDED"},{"id":"autogen_task1_v22","status":"SUCCEEDED"},{"id":"autogen_task1_v24","status":"SUCCEEDED"},{"id":"autogen_task1_v25","status":"SUCCEEDED"},{"id":"autogen_task1_v26","status":"SUCCEEDED"},{"id":"autogen_task1_v27","status":"SUCCEEDED"},{"id":"autogen_task1_v28","status":"SUCCEEDED"},{"id":"autogen_task1_v29","status":"SUCCEEDED"},{"id":"autogen_task1_v30","status":"SUCCEEDED"},{"id":"autogen_task1_v31","status":"SUCCEEDED"},{"id":"autogen_task1_v32","status":"SUCCEEDED"},{"id":"autogen_task1_v33","status":"SUCCEEDED"},{"id":"autogen_task1_v34","status":"SUCCEEDED"},{"id":"autogen_task1_v35","status":"SUCCEEDED"},{"id":"autogen_task1_v36","status":"SUCCEEDED"},{"id":"autogen_task1_v37","status":"SUCCEEDED"},{"id":"autogen_task1_v38","status":"SUCCEEDED"},{"id":"autogen_task1_v40","status":"SUCCEEDED"},{"id":"autogen_task1_v41","status":"SUCCEEDED"},{"id":"autogen_task1_v42","status":"SUCCEEDED"},{"id":"autogen_task1_v43","status":"SUCCEEDED"},{"id":"autogen_task1_v39","status":"SUCCEEDED"},{"id":"autogen_task1_v44","status":"SUCCEEDED"}]},{"id":"autogen_plot_for_task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":1.164076,"curves":[{"id":"autogen_curve_task1_GLC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_F6P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FBP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DPG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PEP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_PYR_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_AMP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_LAC","status":"SUCCEEDED"},{"id":"autogen_curve_task1_G3P","status":"SUCCEEDED"},{"id":"autogen_curve_task1_DHAP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OXA_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Asp_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glu_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OG_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mal_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Acetyl_CoA_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CoA_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IsoCitcyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cit_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ADP_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADH_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADP_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADPH_cyt","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pyr","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CO2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_CoA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Acetyl_CoA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Pi","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Fum","status":"SUCCEEDED"},{"id":"autogen_curve_task1_SCoA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Suc","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GTP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_GDP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Ala","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Asp","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Glu","status":"SUCCEEDED"},{"id":"autogen_curve_task1_H2O","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ETFred","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ETFox","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FADH2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_FAD","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OG","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Mal","status":"SUCCEEDED"},{"id":"autogen_curve_task1_OXA","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cit","status":"SUCCEEDED"},{"id":"autogen_curve_task1_IsoCit","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ATP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_ADP","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADP_p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADPH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NAD_p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_NADH","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Q","status":"SUCCEEDED"},{"id":"autogen_curve_task1_QH2","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cytc3p","status":"SUCCEEDED"},{"id":"autogen_curve_task1_Cytc2p","status":"SUCCEEDED"}]}]}]}