[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    435      0 --:--:-- --:--:-- --:--:--   435
100   139  100   139    0     0    435      0 --:--:-- --:--:-- --:--:--   434

100 31995  100 31995    0     0  75579      0 --:--:-- --:--:-- --:--:-- 75579

[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>
 INFO (CLIStandalone:38) - Starting Vcell... []{}
 INFO (PropertyLoader:578) - Can't read propertyFile /usr/lib/jvm/java-8-openjdk-amd64/jre/vcell.properties specified by java home directory []{}
 INFO (PropertyLoader:584) - ServerID=7.3.0.16, SoftwareVersion=7.5.0.37 []{}
 INFO (BiosimulationsCommand:98) - Beginning execution []{}
 INFO (CLIPythonManager:116) - Initializing Python... []{}
 INFO (CLIPythonManager:136) - Python initialization success! []{}
 INFO (ExecuteImpl:100) - Preparing output directory... []{}
ERROR (RunUtils:507) - java.lang.Exception: File '/root/outputs' could not be deleted! []{}
 INFO (ExecutionJob:86) - Executing OMEX archive /root/archive.omex []{}
-----------------------------------------------------------------------------------------------------
 INFO (NativeLib:29) - Loading combinej []{}
 INFO (RunUtils:475) - TempPath Created: /tmp/vcell_temp_b0434aba-16bc-4e49-99a4-f652729a90214866505820293258681 []{}
 INFO (SedmlJob:104) - Initializing SED-ML document... []{}
 WARN (SEDMLReader:249) - Unexpected [Element: <notes [Namespace: http://sed-ml.org/sed-ml/level1/version2]/>] []{}
 INFO (SedmlJob:117) - Processing SED-ML: VCDB_116898345_Jung_ProcNatlAcadSciUSA_2017997379761607318673.sedml []{}
 INFO (SedmlJob:153) - 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:158) - Successful translation of SED-ML file : VCDB_116898345_Jung_ProcNatlAcadSciUSA_2017997379761607318673.sedml []{}
-----------------------------------------------------------------------------------------------------
 INFO (SedmlJob:162) - Creating pseudo SED-ML for HDF5 conversion... []{}
 INFO (SedmlJob:174) - Creating Biomodel from pseudo SED-ML []{}
 INFO (SedmlJob:235) - Building solvers and starting simulation of all tasks...  []{}
 WARN (SEDMLReader:249) - Unexpected [Element: <notes [Namespace: http://sed-ml.org/sed-ml/level1/version2]/>] []{}
 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}
 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}
 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}
 INFO (SEDMLImporter:182) - Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}
taskToSimulationMap: 1
taskToListOfSubTasksMap: 1
taskToVariableMap: 1
topTaskToBaseTask: 1
 INFO (SolverHandler:422) - Solver: cbit.vcell.solver.ode.CVodeSolverStandalone@73d4066e []{}
 INFO (SolverHandler:423) - Status: Finished: SOLVER_FINISHED:completed []{}
 INFO (SolverHandler:469) - Succesful execution: Model 'archive_VCDB_116898345_Jung_ProcNatlAcadSciUSA_2017997379761607318673.sedml_Application0' Task 'Pin1-FLw/p131_first titration point'. []{}
 INFO (SolverHandler:481) - Running simulation Pin1-FLw/p131_first titration point, 364 ms []{}
-----------------------------------------------------------------------------------------------------
 INFO (SolverHandler:594) - Ran 1 simulation jobs for 1 biomodels. []{}
 INFO (SedmlJob:268) - Generating outputs...  []{}
 INFO (SedmlJob:322) - Generating CSV file...  []{}
 INFO (RunUtils:194) - Ignoring unsupported output `plot2d_Pin1_FLw_p131_first_titration_point` while CSV generation. []{}
 INFO (RunUtils:200) - Generating report `report_Pin1_FLw_p131_first_titration_point`. []{}
 INFO (RunUtils:380) - created csv file for report report_Pin1_FLw_p131_first_titration_point: /root/outputs/VCDB_116898345_Jung_ProcNatlAcadSciUSA_2017997379761607318673.sedml/report_Pin1_FLw_p131_first_titration_point.csv []{}
 INFO (RunUtils:200) - Generating report `__plot__plot2d_Pin1_FLw_p131_first_titration_point`. []{}
 INFO (RunUtils:380) - created csv file for report __plot__plot2d_Pin1_FLw_p131_first_titration_point: /root/outputs/VCDB_116898345_Jung_ProcNatlAcadSciUSA_2017997379761607318673.sedml/__plot__plot2d_Pin1_FLw_p131_first_titration_point.csv []{}
 INFO (SedmlJob:344) - Generating Plots...  []{}
 WARN (CLIPythonManager:78) - Using old style python invocation! []{}
 WARN (CLIPythonManager:250) - Temp out file didn't delete properly []{}
 WARN (CLIPythonManager:251) - Temp error file didn't delete properly []{}
 INFO (SedmlJob:356) - Generating HDF5 file...  []{}
 INFO (NonspatialResultsConverter:202) - Ignoring unsupported output `plot2d_Pin1_FLw_p131_first_titration_point` while CSV generation. []{}
 INFO (SpatialResultsConverter:155) - Ignoring unsupported output `plot2d_Pin1_FLw_p131_first_titration_point` while CSV generation. []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:53) - Was not able to find simulation data for task with ID: tsk_0_0 []{}
 WARN (SpatialResultsConverter:115) - We encountered non-compatible (or non-existent) data. This may mean a problem has been encountered. []{}
 INFO (SedmlJob:308) - Archiving result files []{}
 INFO (RunUtils:449) - Archiving resultant PDF files to `plots.zip`. []{}
 INFO (RunUtils:449) - Archiving resultant CSV files to `reports.zip`. []{}
 INFO (SedmlJob:315) - SED-ML : VCDB_116898345_Jung_ProcNatlAcadSciUSA_2017997379761607318673.sedml successfully completed []{}
 INFO (ExecutionJob:142) - Processing of SedML succeeded.
org.vcell.cli.run.SedmlStatistics@1e0895f5 []{}
 INFO (NativeLib:29) - Loading jhdf5 []{}
 INFO (Hdf5Writer:42) - Creating hdf5 file `reports.h5` in/root/outputs []{}
 INFO (Hdf5Writer:108) - HDF5 file successfully written to. []{}
 INFO (ExecutionJob:171) - Omex archive.omex processing completed (10s) []{}

[0;36m===================================================== Saving log ====================================================[0m
Completed 7.9 KiB/7.9 KiB (63.9 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/649b5322642531fcf940a7da/rawLog.txt
Completed 2.2 KiB/2.2 KiB (18.2 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/649b5322642531fcf940a7da/outputs/log.yml

[0;36m================================================== Zipping outputs ==================================================[0m
  adding: outputs/ (stored 0%)
