[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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100   139  100   139    0     0    226      0 --:--:-- --:--:-- --:--:--   226

100  8269  100  8269    0     0  11480      0 --:--:-- --:--:-- --:--:-- 11480

[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_3832e94e-5af8-400e-a11d-a2d36f11aac711100787425017224384 []{}
 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_903ec509-831a-41e0-8e66-439d87276704927788665564202359 []{}
 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: BIOMD0000000001_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 : BIOMD0000000001_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 (SBMLImporter:966) - adjustExpression(): replacing '___TIME_SYMBOL___' with 't' in (___TIME_SYMBOL___ > t2) []{}
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@756b2d90 []{}
 INFO (SolverHandler:431) - Status: Finished: SOLVER_FINISHED:completed []{}
 INFO (SolverHandler:477) - Succesful execution: Model 'archive_BIOMD0000000001_url.sedml_BIOMD0000000001_url' Task 'task1'. []{}
 INFO (SolverHandler:489) - Running simulation task1_task1, 3209 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_1946594337b16961352362271281245/BIOMD0000000001_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_1946594337b16961352362271281245/BIOMD0000000001_url.sedml/__plot__autogen_plot_for_task1.csv []{}
 INFO (SedmlJob:380) - Generating Plots...  []{}
 WARN (CLIPythonManager:170) - Error calling python: null []{}
 WARN (CLIPythonManager:171) - Attempting to acknowledge warnings / prompts. []{}
 INFO (CLIPythonManager:177) - Second python attempt successful! []{}
 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 : BIOMD0000000001_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_1946594337b16961352362271281245 []{}
 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 (31s) []{}

[0;36m===================================================== Saving log ====================================================[0m
Completed 6.5 KiB/6.5 KiB (73.3 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67868c50ba5a3f02b9f300b0/rawLog.txt

[0;36m===================================================== Saving Structured log ==========================================[0m
Completed 5.1 KiB/5.1 KiB (59.6 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/67868c50ba5a3f02b9f300b0/outputs/log.yml

[0;36m================================================== Zipping outputs ==================================================[0m
  adding: outputs/ (stored 0%)
  adding: outputs/log.yml (deflated 88%)
  adding: outputs/reports.zip (stored 0%)
  adding: outputs/BIOMD0000000001_url.sedml/ (stored 0%)
  adding: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.pdf (deflated 28%)
  adding: outputs/BIOMD0000000001_url.sedml/autogen_plot_for_task1.csv (deflated 74%)
  adding: outputs/BIOMD0000000001_url.sedml/autogen_report_for_task1.csv (deflated 85%)
  adding: outputs/log.json (deflated 95%)
  adding: outputs/reports.h5 (deflated 86%)
