[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    487      0 --:--:-- --:--:-- --:--:--   487

100  8231  100  8231    0     0  20667      0 --:--:-- --:--:-- --:--:-- 20667

[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:92) - Beginning execution []{}
 INFO (CLIPythonManager:116) - Initializing Python... []{}
 INFO (CLIPythonManager:136) - Python initialization success! []{}
 INFO (ExecuteImpl:133) - Preparing output directory... []{}
ERROR (RunUtils:508) - java.lang.Exception: File '/root/outputs' could not be deleted! []{}
 INFO (ExecutionJob:84) - Executing OMEX archive /root/archive.omex []{}
-----------------------------------------------------------------------------------------------------
 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_ec84538d-4767-4bfc-a920-946dee234a8615842134608936751059 []{}
ERROR (ExecutionJob:101) - Error for archive /root/archive.omex []{}
 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message
ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
java.lang.RuntimeException: Error for archive /root/archive.omex
	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:252) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [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.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 
	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	... 14 more
Caused by: java.nio.file.FileSystemException: /metadata.rdf: Read-only file system
	at java.base/sun.nio.fs.UnixException.translateToIOException(Unknown Source) ~[?:?]
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source) ~[?:?]
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source) ~[?:?]
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(Unknown Source) ~[?:?]
	at java.base/java.nio.file.spi.FileSystemProvider.newOutputStream(Unknown Source) ~[?:?]
	at java.base/java.nio.file.Files.newOutputStream(Unknown Source) ~[?:?]
	at java.base/java.nio.file.Files.write(Unknown Source) ~[?:?]
	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:88) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
	... 14 more
srun: error: xanadu-69: task 0: Exited with exit code 1
srun: Terminating job step 8581703.1

[0;36m===================================================== Saving log ====================================================[0m
Completed 5.7 KiB/5.7 KiB (74.9 KiB/s) with 1 file(s) remaining
upload: ./rawLog.txt to s3://files.biosimulations.org/simulations/67323be0b678b3883bb6c155/rawLog.txt

[0;36m===================================================== Saving Structured log ==========================================[0m
Completed 4.5 KiB/4.5 KiB (58.9 KiB/s) with 1 file(s) remaining
upload: outputs/log.yml to s3://files.biosimulations.org/simulations/67323be0b678b3883bb6c155/outputs/log.yml

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