[0;36mThank you for using runBioSimulations![0m

[0;36m================================================ Loading Singularity ================================================[0m

[0;36m=================================================== Set up storage ==================================================[0m

[0;36m========================================== Downloading COMBINE/OMEX archive =========================================[0m
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   139  100   139    0     0    270      0 --:--:-- --:--:-- --:--:--   269

100  5637  100  5637    0     0   9057      0 --:--:-- --:--:-- --:--:--  9057

[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================[0m
INFO:    Using cached SIF image
docker: Command recieved::<-i /root/archive.omex -o /root/outputs>
<-i>
Default case selected
VCell shall execute <biosimulations -i /root/archive.omex -o /root/outputs>
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
 INFO (CLIStandalone:36) - Starting Vcell... []{}
 INFO (BiosimulationsCommand:94) - Beginning execution []{}
 INFO (CLIPythonManager:125) - Initializing Python... []{}
 INFO (CLIPythonManager:150) - Python initialization success! []{}
 INFO (ExecuteImpl:134) - Preparing output directory... []{}
 INFO (ExecutionJob:83) - Executing OMEX archive `archive.omex` []{}
 INFO (ExecutionJob:84) - Archive location: /root/archive.omex []{}
-----------------------------------------------------------------------------------------------------
 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_e214ab64-2c65-4b9d-b080-2577b96bb93d13439997866225184007 []{}
 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_21dd006b-2655-4561-90c6-30643a8ba8866800796035023920810 []{}
 INFO (SedmlJob:110) - Initializing SED-ML document... []{}
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000138_url.sedml []{}
 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)
 []{}
 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000138_url.sedml []{}
-----------------------------------------------------------------------------------------------------
 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}
 INFO (SedmlJob:186) - Creating Biomodel from pseudo SED-ML []{}
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
 INFO (SedmlJob:261) - Building solvers and starting simulation of all tasks...  []{}
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
 INFO (SimulationContext:3289) - mathMapping: message = transforming the Rate Rules... []{}
ERROR (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 []{}
taskToSimulationMap: 1
taskToListOfSubTasksMap: 1
taskToVariableMap: 1
topTaskToBaseTask: 1
 INFO (SolverHandler:430) - Solver: cbit.vcell.solvers.CombinedSundialsSolver@77b3752b []{}
 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}
 INFO (SolverHandler:477) - Succesful execution: Model 'archive_BIOMD0000000138_url.sedml_BIOMD0000000138_url' Task 'task1'. []{}
 INFO (SolverHandler:489) - Running simulation task1_task1, 865 ms []{}
-----------------------------------------------------------------------------------------------------
 INFO (SolverHandler:613) - Ran 1 simulation jobs for 1 biomodels. []{}
 INFO (SedmlJob:302) - Generating outputs...  []{}
 INFO (SedmlJob:357) - Generating CSV file...  []{}
 INFO (RunUtils:196) - Ignoring unsupported output `autogen_plot_for_task1` while CSV generation. []{}
 INFO (RunUtils:202) - Generating report `autogen_report_for_task1`. []{}
 INFO (RunUtils:381) - created csv file for report autogen_report_for_task1: /tmp/VCell_CLI_194659db20a7077861949965531634/BIOMD0000000138_url.sedml/autogen_report_for_task1.csv []{}
 INFO (RunUtils:202) - Generating report `__plot__autogen_plot_for_task1`. []{}
 INFO (RunUtils:381) - created csv file for report __plot__autogen_plot_for_task1: /tmp/VCell_CLI_194659db20a7077861949965531634/BIOMD0000000138_url.sedml/__plot__autogen_plot_for_task1.csv []{}
 INFO (SedmlJob:380) - Generating Plots...  []{}
 INFO (SedmlJob:391) - Generating HDF5 file...  []{}
 INFO (NonspatialResultsConverter:204) - Ignoring unsupported output `autogen_plot_for_task1` while CSV generation. []{}
 INFO (SedmlJob:343) - Archiving result files []{}
 INFO (RunUtils:450) - Archiving resultant PDF files to `plots.zip`. []{}
 INFO (RunUtils:450) - Archiving resultant CSV files to `reports.zip`. []{}
 INFO (SedmlJob:350) - SED-ML : BIOMD0000000138_url.sedml successfully completed []{}
 INFO (ExecutionJob:144) - Processing of SedML succeeded.
	> 1 model
	> 1 simulation
	> 1 task
	> 2 outputs
		>> 1 report
		>> 1 2D plot
		>> 0 3D plots
	> Does not have Math Overrides
	> Does not have Parameter Scans []{}
 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_194659db20a7077861949965531634 []{}
 WARN (WritableHdfFile:50) - Writing files is in alpha. Check files carefully! []{}
 INFO (BiosimulationsHdf5Writer:122) - HDF5 file successfully written to. []{}
 INFO (ExecutionJob:174) - Omex archive.omex processing completed (11s) []{}

[0;36m===================================================== Saving log ====================================================[0m
Completed 6.3 KiB/6.3 KiB (65.5 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67868ebf167dc18b5b24863e/rawLog.txt

[0;36m===================================================== Saving Structured log ==========================================[0m
Completed 3.3 KiB/3.3 KiB (15.9 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/67868ebf167dc18b5b24863e/outputs/log.yml

[0;36m================================================== Zipping outputs ==================================================[0m
  adding: outputs/ (stored 0%)
  adding: outputs/log.yml (deflated 84%)
  adding: outputs/BIOMD0000000138_url.sedml/ (stored 0%)
  adding: outputs/BIOMD0000000138_url.sedml/autogen_plot_for_task1.pdf (deflated 20%)
  adding: outputs/BIOMD0000000138_url.sedml/autogen_plot_for_task1.csv (deflated 64%)
  adding: outputs/BIOMD0000000138_url.sedml/autogen_report_for_task1.csv (deflated 70%)
  adding: outputs/reports.zip (stored 0%)
  adding: outputs/log.json (deflated 93%)
  adding: outputs/reports.h5 (deflated 67%)
