{"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\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100  9542  100  9542    0     0  22862      0 --:--:-- --:--:-- --:--:--  125k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\n \u001b[34msucceeded\u001b[0m\n\n  Executed 2 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 2\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 (2):\n    Succeeded: 2\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/674dc73010bb4455d61877b0/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 6.6 KiB/6.6 KiB (69.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/674dc73010bb4455d61877b0/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 83%)\n  adding: outputs/Adlung2021 _model_jakstat_pa.sedml/ (stored 0%)\n  adding: outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.pdf (deflated 32%)\n  adding: outputs/reports.h5 (deflated 34%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 150.4 KiB/150.4 KiB (1.6 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/674dc73010bb4455d61877b0/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 8.3 KiB/134.4 KiB (81.6 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/674dc73010bb4455d61877b0/outputs/plots.zip\nCompleted 8.3 KiB/134.4 KiB (81.6 KiB/s) with 3 file(s) remaining\rCompleted 20.8 KiB/134.4 KiB (160.7 KiB/s) with 3 file(s) remaining\rupload: outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.pdf to s3://files.biosimulations.org/simulations/674dc73010bb4455d61877b0/outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.pdf\nCompleted 20.8 KiB/134.4 KiB (160.7 KiB/s) with 2 file(s) remaining\rCompleted 131.5 KiB/134.4 KiB (955.2 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/674dc73010bb4455d61877b0/output.zip\nCompleted 131.5 KiB/134.4 KiB (955.2 KiB/s) with 1 file(s) remaining\rCompleted 134.4 KiB/134.4 KiB (905.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc73010bb4455d61877b0/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/Adlung2021 _model_jakstat_pa.sedml  \n  inflating: contents/Adlung2021 _model_jakstat_pa.xml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 39.4 KiB/141.4 KiB (506.4 KiB/s) with 3 file(s) remaining\rupload: contents/Adlung2021 _model_jakstat_pa.sedml to s3://files.biosimulations.org/simulations/674dc73010bb4455d61877b0/contents/Adlung2021 _model_jakstat_pa.sedml\nCompleted 39.4 KiB/141.4 KiB (506.4 KiB/s) with 2 file(s) remaining\rCompleted 40.1 KiB/141.4 KiB (331.8 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/674dc73010bb4455d61877b0/contents/manifest.xml\nCompleted 40.1 KiB/141.4 KiB (331.8 KiB/s) with 1 file(s) remaining\rCompleted 141.4 KiB/141.4 KiB (902.1 KiB/s) with 1 file(s) remaining\rupload: contents/Adlung2021 _model_jakstat_pa.xml to s3://files.biosimulations.org/simulations/674dc73010bb4455d61877b0/contents/Adlung2021 _model_jakstat_pa.xml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 5.3 KiB/5.3 KiB (66.5 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc73010bb4455d61877b0/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.\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;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":2.003138,"sedDocuments":[{"location":"Adlung2021 _model_jakstat_pa.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 2 tasks, 1 reports, and 1 plots:\r\n  Adlung2021 _model_jakstat_pa.sedml:\r\n    Tasks (2):\r\n      task1\r\n      task2\r\n    Reports (1):\r\n      autogen_report_for_task2: 71 data sets\r\n    Plots (1):\r\n      plot_2_task2: 2 curves\r\n\r\nExecuting SED-ML file 1: Adlung2021 _model_jakstat_pa.sedml ...\r\n  Found 2 tasks and 2 outputs:\r\n    Tasks:\r\n      `task1`\r\n      `task2`\r\n    Outputs:\r\n      `autogen_report_for_task2`\r\n      `plot_2_task2`\r\n  Executing task 1: `task1`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `plot_2_task2` ... \u001b[36mqueued\u001b[0m\r\n      Generating output 2: `autogen_report_for_task2` ... \u001b[36mqueued\u001b[0m\r\n  Executing task 2: `task2`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `plot_2_task2` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `autogen_report_for_task2` ...","duration":1.536872,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.242318,"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":100000},{"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}]},{"id":"task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.173827,"algorithm":null,"simulatorDetails":null}],"outputs":[{"id":"plot_2_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.171614,"curves":[{"id":"p1_curve_1_task2","status":"SUCCEEDED"},{"id":"p1_curve_2_task2","status":"SUCCEEDED"}]},{"id":"autogen_report_for_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"","duration":0.310442,"dataSets":[{"id":"autogen_time_for_task2","status":"SUCCEEDED"},{"id":"autogen_task2_measuralbe_pSTAT5","status":"SUCCEEDED"},{"id":"autogen_task2__pSTAT5_Total_STAT5","status":"SUCCEEDED"},{"id":"autogen_task2_EpoRJAK2","status":"SUCCEEDED"},{"id":"autogen_task2_EpoRpJAK2","status":"SUCCEEDED"},{"id":"autogen_task2_p1EpoRpJAK2","status":"SUCCEEDED"},{"id":"autogen_task2_p2EpoRpJAK2","status":"SUCCEEDED"},{"id":"autogen_task2_p12EpoRpJAK2","status":"SUCCEEDED"},{"id":"autogen_task2_SHP1","status":"SUCCEEDED"},{"id":"autogen_task2_SHP1Act","status":"SUCCEEDED"},{"id":"autogen_task2_STAT5","status":"SUCCEEDED"},{"id":"autogen_task2_pSTAT5","status":"SUCCEEDED"},{"id":"autogen_task2_npSTAT5","status":"SUCCEEDED"},{"id":"autogen_task2_CISnRNA1","status":"SUCCEEDED"},{"id":"autogen_task2_CISnRNA2","status":"SUCCEEDED"},{"id":"autogen_task2_CISRNA","status":"SUCCEEDED"},{"id":"autogen_task2_CIS","status":"SUCCEEDED"},{"id":"autogen_task2_SOCS3","status":"SUCCEEDED"},{"id":"autogen_task2_ActD","status":"SUCCEEDED"},{"id":"autogen_task2_CISEqc","status":"SUCCEEDED"},{"id":"autogen_task2_CISInh","status":"SUCCEEDED"},{"id":"autogen_task2_CISRNADelay","status":"SUCCEEDED"},{"id":"autogen_task2_CISRNAEqc","status":"SUCCEEDED"},{"id":"autogen_task2_CISRNATurn","status":"SUCCEEDED"},{"id":"autogen_task2_CISTurn","status":"SUCCEEDED"},{"id":"autogen_task2_DeaEpoRJAKActSHP1","status":"SUCCEEDED"},{"id":"autogen_task2_EpoRActJAK2","status":"SUCCEEDED"},{"id":"autogen_task2_JAK2ActEpo","status":"SUCCEEDED"},{"id":"autogen_task2_SHP1ActEpoR","status":"SUCCEEDED"},{"id":"autogen_task2_SHP1Dea","status":"SUCCEEDED"},{"id":"autogen_task2_SOCS3Eqc","status":"SUCCEEDED"},{"id":"autogen_task2_SOCS3EqcOE","status":"SUCCEEDED"},{"id":"autogen_task2_SOCS3Inh","status":"SUCCEEDED"},{"id":"autogen_task2_SOCS3Turn","status":"SUCCEEDED"},{"id":"autogen_task2_SOCS3oe","status":"SUCCEEDED"},{"id":"autogen_task2_STAT5ActEpoR","status":"SUCCEEDED"},{"id":"autogen_task2_STAT5ActJAK2","status":"SUCCEEDED"},{"id":"autogen_task2_STAT5Exp","status":"SUCCEEDED"},{"id":"autogen_task2_STAT5Imp","status":"SUCCEEDED"},{"id":"autogen_task2_epo_level","status":"SUCCEEDED"},{"id":"autogen_task2_init_EpoRJAK2","status":"SUCCEEDED"},{"id":"autogen_task2_init_SHP1","status":"SUCCEEDED"},{"id":"autogen_task2_init_STAT5","status":"SUCCEEDED"},{"id":"autogen_task2_Epo","status":"SUCCEEDED"},{"id":"autogen_task2_Total_STAT5","status":"SUCCEEDED"},{"id":"autogen_task2_cyt","status":"SUCCEEDED"},{"id":"autogen_task2_nuc","status":"SUCCEEDED"},{"id":"autogen_task2_v1_v_0","status":"SUCCEEDED"},{"id":"autogen_task2_v2_v_1","status":"SUCCEEDED"},{"id":"autogen_task2_v3_v_2","status":"SUCCEEDED"},{"id":"autogen_task2_v4_v_3","status":"SUCCEEDED"},{"id":"autogen_task2_v5_v_4","status":"SUCCEEDED"},{"id":"autogen_task2_v6_v_5","status":"SUCCEEDED"},{"id":"autogen_task2_v7_v_6","status":"SUCCEEDED"},{"id":"autogen_task2_v8_v_7","status":"SUCCEEDED"},{"id":"autogen_task2_v9_v_8","status":"SUCCEEDED"},{"id":"autogen_task2_v12_v_11","status":"SUCCEEDED"},{"id":"autogen_task2_v13_v_12","status":"SUCCEEDED"},{"id":"autogen_task2_v14_v_13","status":"SUCCEEDED"},{"id":"autogen_task2_v15_v_14","status":"SUCCEEDED"},{"id":"autogen_task2_v16_v_15","status":"SUCCEEDED"},{"id":"autogen_task2_v17_v_16","status":"SUCCEEDED"},{"id":"autogen_task2_v18_v_17","status":"SUCCEEDED"},{"id":"autogen_task2_v19_v_18","status":"SUCCEEDED"},{"id":"autogen_task2_v20_v_19","status":"SUCCEEDED"},{"id":"autogen_task2_v21_v_20","status":"SUCCEEDED"},{"id":"autogen_task2_v22_v_21","status":"SUCCEEDED"},{"id":"autogen_task2_v23_v_22","status":"SUCCEEDED"},{"id":"autogen_task2_v24_v_23","status":"SUCCEEDED"},{"id":"autogen_task2_v25_v_24","status":"SUCCEEDED"},{"id":"autogen_task2_v26_v_25","status":"SUCCEEDED"}]}]}]}