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For the (-b) option you specified a location which cannot be written to #26

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. ./interproscan.sh -i test_proteins.fasta -f tsv -appl gene3d
2.
3.

What is the expected output? What do you see instead?

09/08/2013 13:59:49 Welcome to InterProScan 5RC6
Running the following analyses:
[jobGene3d-3.5.0]
Can write test.
For the (-b) option you specified a location which cannot be written to:
/opt/ngs/interproscan/test_proteins.fasta

What version of the product are you using? On what operating system?
InterProScan 5RC6, SUSE LINUX Enterprise x86_64

Please provide any additional information below.

When i run the same command adding the -b option like this './interproscan.sh 
-i test_proteins.fasta -f tsv -appl gene3d -b TEST/test'

I get this output instead:

09/08/2013 14:07:14 Welcome to InterProScan 5RC6
Running the following analyses:
[jobGene3d-3.5.0]
Running InterProScan v5 in STANDALONE mode...
2013-08-09 14:07:37,186 
[uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener:106] ERROR - Execution 
thrown when attempting to executeInTransaction the StepExecution.  All database 
activity rolled back.
java.lang.IllegalStateException: Directory temp/uranos_20130809_140737180_an7m 
could not be created while configuring temp/[UNIQUE]
        at uk.ac.ebi.interpro.scan.io.TemporaryDirectoryManagerImpl.replacePath(TemporaryDirectoryManagerImpl.java:66)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.getValidWorkingDirectory(StepExecutionTransactionImpl.java:114)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:84)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
        at com.sun.proxy.$Proxy94.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1071)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1063)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:960)
        at java.lang.Thread.run(Unknown Source)
2013-08-09 14:07:37,407 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:48] WARN - 
StepInstance 1 is being re-run following a failure.
2013-08-09 14:07:37,422 
[uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener:106] ERROR - Execution 
thrown when attempting to executeInTransaction the StepExecution.  All database 
activity rolled back.
java.lang.IllegalStateException: Directory temp/uranos_20130809_140737180_an7m 
could not be created while configuring temp/[UNIQUE]
        at uk.ac.ebi.interpro.scan.io.TemporaryDirectoryManagerImpl.replacePath(TemporaryDirectoryManagerImpl.java:66)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.getValidWorkingDirectory(StepExecutionTransactionImpl.java:114)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:84)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
        at com.sun.proxy.$Proxy94.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1071)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1063)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:960)
        at java.lang.Thread.run(Unknown Source)
2013-08-09 14:07:37,649 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL 
- Analysis step 1 : Load proteins from a fasta file and create required 
JobInstance objects for proteins null to null has failed irretrievably.  
Available StackTraces follow.
2013-08-09 14:07:37,650 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL 
- The JVM will now exit with a non-zero exit status.

What am I missing?

Original issue reported on code.google.com by PMassa...@gmail.com on 9 Aug 2013 at 12:09

GoogleCodeExporter commented 9 years ago 
It looks like the temp directory you are using is not writable, hence the 
excecption that you get. The default location for this directory is the temp 
subdirectory in your interproscan installation. I'd check first if you have 
permissions to write files there.

If you cannot write there and can't change the permissions, you can change the 
temp directory location by using the -T option on the commandline, or by 
changing the temporary.file.directory property in the interproscan.properties 
file.

Hope this helps,
Craig

Original comment by interpro...@googlemail.com on 9 Aug 2013 at 12:45

GoogleCodeExporter commented 9 years ago 
Hey Craig,

Thanks for your help, i changed the permissions, it all works fine now.

Thanks again,
Mathieu

Original comment by PMassa...@gmail.com on 9 Aug 2013 at 1:59

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 15 Aug 2013 at 11:17

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 15 Aug 2013 at 11:21

GoogleCodeExporter commented 9 years ago 
Resolved.

Original comment by Maxim.Sc...@gmail.com on 25 Sep 2013 at 11:14