[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  1989  100  1989    0     0   4361      0 --:--:-- --:--:-- --:--:--  4361

[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:95) - Beginning execution []{}
 INFO (CLIPythonManager:116) - Initializing Python... []{}
 INFO (CLIPythonManager:136) - Python initialization success! []{}
 INFO (ExecuteImpl:134) - Preparing output directory... []{}
 INFO (ExecutionJob:84) - Executing OMEX archive /root/archive.omex []{}
-----------------------------------------------------------------------------------------------------
 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_a574f13d-3b09-4c70-a7c8-24212fd226248300984646154271904 []{}
 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_561ba7c3-38d0-4986-8d5e-75dfe033a2d914950216803833835696 []{}
 INFO (SedmlJob:110) - Initializing SED-ML document... []{}
 INFO (SedmlJob:125) - Processing SED-ML: tmp453561 []{}
 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 : tmp453561 []{}
-----------------------------------------------------------------------------------------------------
 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}
ERROR (SedmlJob:461) - Failed to create file /tmp/VCell_CLI_1934f627c7110877600117278273547/temp/simulation_tmp453561 []{}
java.lang.RuntimeException: Failed to create file /tmp/VCell_CLI_1934f627c7110877600117278273547/temp/simulation_tmp453561
	at org.vcell.cli.run.SedmlJob.preProcessDoc(SedmlJob.java:178) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:133) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
ERROR (ExecutionJob:135) - Statistics of failed SedML:
org.vcell.cli.run.SedmlStatistics@4f824872 []{}
 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}
ERROR (SedmlJob:273) - Cannot invoke "org.jlibsedml.SedML.getPathForURI()" because "this.sedml" is null []{}
java.lang.NullPointerException: Cannot invoke "org.jlibsedml.SedML.getPathForURI()" because "this.sedml" is null
	at org.vcell.sedml.SEDMLImporter.initialize(SEDMLImporter.java:107) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.sedml.SEDMLImporter.<init>(SEDMLImporter.java:94) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:328) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
 INFO (SedmlJob:298) - Generating outputs...  []{}
 INFO (SedmlJob:387) - Generating HDF5 file...  []{}
ERROR (SedmlJob:461) - Cannot invoke "org.jlibsedml.SedML.getPathForURI()" because "sedml" is null []{}
java.lang.NullPointerException: Cannot invoke "org.jlibsedml.SedML.getPathForURI()" because "sedml" is null
	at org.vcell.cli.run.hdf5.Hdf5DataExtractor.<init>(Hdf5DataExtractor.java:40) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.SedmlJob.generateHDF5(SedmlJob.java:389) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:305) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:235) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
 WARN (SedmlJob:238) - Outputs could not be processed. []{}
org.vcell.cli.exceptions.ExecutionException: error while processing outputs: Cannot invoke "org.jlibsedml.SedML.getPathForURI()" because "sedml" is null
	at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:317) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:235) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
Caused by: java.lang.NullPointerException: Cannot invoke "org.jlibsedml.SedML.getPathForURI()" because "sedml" is null
	at org.vcell.cli.run.hdf5.Hdf5DataExtractor.<init>(Hdf5DataExtractor.java:40) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.SedmlJob.generateHDF5(SedmlJob.java:389) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.SedmlJob.processOutputs(SedmlJob.java:305) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	... 16 more
ERROR (SedmlJob:461) - Failure executing the sed document.  []{}
java.lang.RuntimeException: Failure executing the sed document. 
	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:239) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:99) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:22) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
 WARN (SedmlJob:332) - Cannot invoke "org.jlibsedml.SedML.getPathForURI()" because "this.sedml" is nullCannot invoke "org.jlibsedml.SedML.getPathForURI()" because "sedml" is nullFailure executing the sed document.  []{}
ERROR (ExecutionJob:146) - Processing of SedML has failed.
org.vcell.cli.run.SedmlStatistics@4f824872 []{}
 INFO (BiosimulationsHdf5Writer:39) - Creating hdf5 file `reports.h5` in/tmp/VCell_CLI_1934f627c7110877600117278273547 []{}
 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 (3s) []{}
ERROR (BiosimulationsCommand:103) - Errors occurred during execution []{}
 | Root(root) | OMEX_EXECUTE(archive.omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /tmp/vcell_temp_a574f13d-3b09-4c70-a7c8-24212fd226248300984646154271904/tmp453561 failed with error: 
 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 
 | Root(root) | OMEX_EXECUTE(archive.omex) | PROCESSING_SIMULATION_OUTPUTS(processOutputs) | **** Error: Error processing outputs
srun: error: xanadu-65: task 0: Exited with exit code 1
srun: Terminating job step 8629135.1

[0;36m===================================================== Saving log ====================================================[0m
Completed 14.7 KiB/14.7 KiB (172.4 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/673f54940d09353e8f12a760/rawLog.txt

[0;36m===================================================== Saving Structured log ==========================================[0m
Completed 116 Bytes/116 Bytes (1.5 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/673f54940d09353e8f12a760/outputs/log.yml

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