{"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    471      0 --:--:-- --:--:-- --:--:--   472\n\r  6  9542    6   603    0     0   1455      0  0:00:06 --:--:--  0:00:06  1455\r100  9542  100  9542    0     0  22663      0 --:--:-- --:--:-- --:--:-- 1454k\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\ndocker: Command recieved::<-i /root/archive.omex -o /root/outputs>\n<-i>\nDefault case selected\nVCell shall execute <biosimulations -i /root/archive.omex -o /root/outputs>\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\nWARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release\n INFO (CLIStandalone:36) - Starting Vcell... []{}\n INFO (BiosimulationsCommand:94) - Beginning execution []{}\n INFO (CLIPythonManager:125) - Initializing Python... []{}\n INFO (CLIPythonManager:150) - Python initialization success! []{}\n INFO (ExecuteImpl:134) - Preparing output directory... []{}\n INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}\n INFO (ExecutionJob:84) - Archive location: /root/archive.omex []{}\n-----------------------------------------------------------------------------------------------------\n INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_d6909f0e-c3e5-44f6-b239-2ff8835eebb617490751569131771809 []{}\n INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_1bf2bd03-05ee-48f1-8a5f-508ca596f3f24794341462979698974 []{}\n INFO (SedmlJob:110) - Initializing SED-ML document... []{}\nSED-ML version level not supported, import may fail\nSED-ML version level not supported, import may fail\n INFO (SedmlJob:125) - Processing SED-ML: Adlung2021 _model_jakstat_pa.sedml []{}\n INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 2 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)\n []{}\n INFO (SedmlJob:166) - Successful translation of SED-ML file : Adlung2021 _model_jakstat_pa.sedml []{}\n-----------------------------------------------------------------------------------------------------\n INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}\n INFO (SedmlJob:186) - Creating Biomodel from pseudo SED-ML []{}\nSED-ML version level not supported, import may fail\nSED-ML version level not supported, import may fail\n INFO (SedmlJob:261) - Building solvers and starting simulation of all tasks...  []{}\nSED-ML version level not supported, import may fail\nSED-ML version level not supported, import may fail\n INFO (AbstractMathMapping:1457) - WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique []{}\nERROR (SEDMLImporter:187) - Task (id='task1)' is not compatible, no equivalent solver found in ontology for requested algorithm 'KISAO:0000694'; trying with deterministic default solver CombinedSundials []{}\nERROR (SEDMLImporter:1074) - Algorithm parameter with kisao id 'KISAO:0000571' not supported at this time, skipping. []{}\nERROR (SEDMLImporter:1074) - Algorithm parameter with kisao id 'KISAO:0000216' not supported at this time, skipping. []{}\nERROR (SEDMLImporter:1074) - Algorithm parameter with kisao id 'KISAO:0000415' not supported at this time, skipping. []{}\ntaskToSimulationMap: 1\ntaskToListOfSubTasksMap: 1\ntaskToVariableMap: 1\ntopTaskToBaseTask: 1\n INFO (SolverHandler:430) - Solver: cbit.vcell.solvers.CombinedSundialsSolver@5bf4764d []{}\n INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}\n INFO (SolverHandler:477) - Succesful execution: Model 'archive_Adlung2021 _model_jakstat_pa.sedml_model' Task 'task1'. []{}\n INFO (SolverHandler:489) - Running simulation task1_task1, 262 ms []{}\n-----------------------------------------------------------------------------------------------------\n INFO (SolverHandler:430) - Solver: cbit.vcell.solvers.CombinedSundialsSolver@283ab206 []{}\n INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}\n INFO (SolverHandler:477) - Succesful execution: Model 'archive_Adlung2021 _model_jakstat_pa.sedml_model' Task 'task1'. []{}\n INFO (SolverHandler:489) - Running simulation task1_task1, 71 ms []{}\n-----------------------------------------------------------------------------------------------------\n INFO (SolverHandler:613) - Ran 2 simulation jobs for 1 biomodels. []{}\n INFO (SedmlJob:302) - Generating outputs...  []{}\n INFO (SedmlJob:357) - Generating CSV file...  []{}\n INFO (RunUtils:196) - Ignoring unsupported output `plot_2_task2` while CSV generation. []{}\n INFO (RunUtils:202) - Generating report `autogen_report_for_task2`. []{}\n INFO (RunUtils:381) - created csv file for report autogen_report_for_task2: /tmp/VCell_CLI_19387d2424113745318976273432780/Adlung2021 _model_jakstat_pa.sedml/autogen_report_for_task2.csv []{}\n INFO (RunUtils:202) - Generating report `__plot__plot_2_task2`. []{}\n INFO (RunUtils:381) - created csv file for report __plot__plot_2_task2: /tmp/VCell_CLI_19387d2424113745318976273432780/Adlung2021 _model_jakstat_pa.sedml/__plot__plot_2_task2.csv []{}\n INFO (SedmlJob:380) - Generating Plots...  []{}\n INFO (SedmlJob:391) - Generating HDF5 file...  []{}\n INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `plot_2_task2` while CSV generation. []{}\n INFO (SedmlJob:343) - Archiving result files []{}\n INFO (RunUtils:450) - Archiving resultant PDF files to `plots.zip`. []{}\n INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}\n INFO (SedmlJob:350) - SED-ML : Adlung2021 _model_jakstat_pa.sedml successfully completed []{}\n INFO (ExecutionJob:144) - Processing of SedML succeeded.\n\t> 1 model\n\t> 1 simulation\n\t> 2 tasks\n\t> 2 outputs\n\t\t>> 1 report\n\t\t>> 1 2D plot\n\t\t>> 0 3D plots\n\t> Does not have Math Overrides\n\t> Does not have Parameter Scans []{}\n INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_19387d2424113745318976273432780 []{}\n WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}\n INFO (BiosimulationsHdf5Writer:122) - HDF5 file successfully written to. []{}\n INFO (ExecutionJob:174) - Omex archive.omex processing completed (10s) []{}\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 7.1 KiB/7.1 KiB (93.1 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 5.2 KiB/5.2 KiB (66.8 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/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/reports.zip (stored 0%)\n  adding: outputs/log.json (deflated 93%)\n  adding: outputs/Adlung2021 _model_jakstat_pa.sedml/ (stored 0%)\n  adding: outputs/Adlung2021 _model_jakstat_pa.sedml/autogen_report_for_task2.csv (deflated 80%)\n  adding: outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.pdf (deflated 31%)\n  adding: outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.csv (deflated 79%)\n  adding: outputs/reports.h5 (deflated 75%)\n  adding: rawLog.txt (deflated 72%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/355.4 KiB (6.1 MiB/s) with 1 file(s) remaining\rCompleted 355.4 KiB/355.4 KiB (1.0 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 256.0 KiB/1.0 MiB (4.0 MiB/s) with 8 file(s) remaining\rCompleted 512.0 KiB/1.0 MiB (4.7 MiB/s) with 8 file(s) remaining\rCompleted 525.7 KiB/1.0 MiB (3.9 MiB/s) with 8 file(s) remaining\rupload: outputs/log.json to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/outputs/log.json\nCompleted 525.7 KiB/1.0 MiB (3.9 MiB/s) with 7 file(s) remaining\rCompleted 593.8 KiB/1.0 MiB (4.3 MiB/s) with 7 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/output.zip\nCompleted 593.8 KiB/1.0 MiB (4.3 MiB/s) with 6 file(s) remaining\rCompleted 602.6 KiB/1.0 MiB (4.2 MiB/s) with 6 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/outputs/plots.zip\nCompleted 602.6 KiB/1.0 MiB (4.2 MiB/s) with 5 file(s) remaining\rCompleted 611.4 KiB/1.0 MiB (4.2 MiB/s) with 5 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/rawLog.txt\nCompleted 611.4 KiB/1.0 MiB (4.2 MiB/s) with 4 file(s) remaining\rCompleted 867.4 KiB/1.0 MiB (5.7 MiB/s) with 4 file(s) remaining\rCompleted 879.8 KiB/1.0 MiB (5.3 MiB/s) with 4 file(s) remaining\rupload: outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.pdf to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.pdf\nCompleted 879.8 KiB/1.0 MiB (5.3 MiB/s) with 3 file(s) remaining\rCompleted 990.2 KiB/1.0 MiB (5.3 MiB/s) with 3 file(s) remaining\rupload: outputs/reports.zip to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/outputs/reports.zip\nCompleted 990.2 KiB/1.0 MiB (5.3 MiB/s) with 2 file(s) remaining\rCompleted 1017.7 KiB/1.0 MiB (4.6 MiB/s) with 2 file(s) remaining\rupload: outputs/Adlung2021 _model_jakstat_pa.sedml/autogen_report_for_task2.csv to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/outputs/Adlung2021 _model_jakstat_pa.sedml/autogen_report_for_task2.csv\nCompleted 1017.7 KiB/1.0 MiB (4.6 MiB/s) with 1 file(s) remaining\rCompleted 1.0 MiB/1.0 MiB (3.2 MiB/s) with 1 file(s) remaining   \rupload: outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.csv to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/outputs/Adlung2021 _model_jakstat_pa.sedml/plot_2_task2.csv\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 101.3 KiB/141.4 KiB (995.3 KiB/s) with 3 file(s) remaining\rupload: contents/Adlung2021 _model_jakstat_pa.xml to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/contents/Adlung2021 _model_jakstat_pa.xml\nCompleted 101.3 KiB/141.4 KiB (995.3 KiB/s) with 2 file(s) remaining\rCompleted 102.0 KiB/141.4 KiB (975.5 KiB/s) with 2 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/contents/manifest.xml\nCompleted 102.0 KiB/141.4 KiB (975.5 KiB/s) with 1 file(s) remaining\rCompleted 141.4 KiB/141.4 KiB (906.2 KiB/s) with 1 file(s) remaining\rupload: contents/Adlung2021 _model_jakstat_pa.sedml to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/contents/Adlung2021 _model_jakstat_pa.sedml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 12.4 KiB/12.4 KiB (124.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/674dc733ef911d5d45259bfd/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.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... 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.\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":10,"sedDocuments":[{"location":"Adlung2021 _model_jakstat_pa.sedml","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Initializing SED-ML document... done. Successful translation of SED-ML file. Building solvers and starting simulation of all tasks... Generating outputs... Generating CSV file... Done. Generating HDF5 file...","duration":null,"tasks":[{"id":"task1","status":"SUCCEEDED","exception":null,"skipReason":null,"output":null,"duration":2,"algorithm":"KISAO_0000019","simulatorDetails":null},{"id":"task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":"Initializing simulation job 1 ... done. Starting simulation... done.","duration":2,"algorithm":"KISAO_0000019","simulatorDetails":null}],"outputs":[{"id":"plot_2_task2","status":"SUCCEEDED","exception":null,"skipReason":null,"output":null,"duration":null,"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":null,"duration":null,"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"}]}]}]}