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ips5rc4 combines identical sequences in tsv-output

When annotating multiple identical sequences with different IDs, the domains 
hits are reported using concatenated (with "|") IDs.

Intuitively IPS should report them separately for each input ID.

See the attached files for a simple example.

Original issue reported on code.google.com by [email protected] on 11 Mar 2013 at 1:12

Attachments:

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

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 [email protected] on 9 Aug 2013 at 12:09

[interhelp #21071] failure likely related to blastall

What steps will reproduce the problem?
1. Ubuntu 14.04 gcc 4.8.2
2. test dataset works, though real dataset fails:
3. execute like this: ./interproscan.sh -i 
/mnt/data3/macmanes/STAR/cuffdiff/sig.high.in.dry.fasta -f tsv --goterms 
-iprscan --pathways -o high.in.dry


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


What version of the product are you using? On what operating system?

5.4-47.0

Please provide any additional information below.

01/06/2014 07:01:07:373 Welcome to InterProScan-5.4-47.0
01/06/2014 07:01:26:867 Running the following analyses:
[jobTIGRFAM-13.0, jobProDom-2006.1, jobSMART-6.2, jobHAMAP-201311.27, 
jobPrositePatterns-20.97, jobSuperFamily-1.75, jobPRINTS-42.0, jobPanther-9.0, 
jobGene3d-3.5.0, jobPIRSF-2.84, jobPfamA-27.0, jobPrositeProfiles-20.97, 
jobCoils-2.2]
01/06/2014 07:01:26:874 Running InterProScan v5 in STANDALONE mode...
Loading file /mnt/data3/macmanes/STAR/cuffdiff/sig.high.in.dry.fasta
Available matches will be retrieved from the pre-calculated match lookup 
service.

Matches for any sequences that are not represented in the lookup service will 
be calculated locally.
01/06/2014 08:24:37:697 25% completed
01/06/2014 08:53:13:248 50% completed
01/06/2014 08:55:27:867 75% completed
2014-06-01 08:55:57,511 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:146] 
ERROR - Command line failed with exit code: 134
Command: bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 
-a 4 -d /home/macmanes/interproscan-5.4-47.0/data/pirsf/2.84/sf.seq -i 
/home/macmanes/interproscan-5.4-47.0/temp/davinci_20140601_070135568_9iu4//jobPI
RSF-2.84
/000000000101_000000000150.blastInputFile.fasta
Error output from binary:
libgcc_s.so.1 must be installed for pthread_cancel to work

2014-06-01 08:55:57,518 
[uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] ERROR - 
Execution thrown when attempting to executeInTransaction the StepExecution.  
All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 134
Command: bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 
-a 4 -d /home/macmanes/interproscan-5.4-47.0/data/pirsf/2.84/sf.seq -i 
/home/macmanes/interproscan-5.4-47.0/temp/davinci_20140601_070135568_9iu4//jobPI
RSF-2.84
/000000000101_000000000150.blastInputFile.fasta
Error output from binary:
libgcc_s.so.1 must be installed for pthread_cancel to work

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:148)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
    at sun.reflect.GeneratedMethodAccessor65.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:181)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Thread.java:744)
2014-06-01 08:55:57,843 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:56] WARN - 
StepInstance 331 is being re-run following a failure.
2014-06-01 08:56:17,850 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:146] 
ERROR - Command line failed with exit code: 134
Command: bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 
-a 4 -d /home/macmanes/interproscan-5.4-47.0/data/pirsf/2.84/sf.seq -i 
/home/macmanes/interproscan-5.4-47.0/temp/davinci_20140601_070135568_9iu4//jobPI
RSF-2.84
/000000000151_000000000200.blastInputFile.fasta
Error output from binary:
libgcc_s.so.1 must be installed for pthread_cancel to work

2014-06-01 08:56:17,852 
[uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] ERROR - 
Execution thrown when attempting to executeInTransaction the StepExecution.  
All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 134
Command: bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 
-a 4 -d /home/macmanes/interproscan-5.4-47.0/data/pirsf/2.84/sf.seq -i 
/home/macmanes/interproscan-5.4-47.0/temp/davinci_20140601_070135568_9iu4//jobPI
RSF-2.84
/000000000151_000000000200.blastInputFile.fasta
Error output from binary:
libgcc_s.so.1 must be installed for pthread_cancel to work

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:148)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
    at sun.reflect.GeneratedMethodAccessor65.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:181)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Thread.java:744)
2014-06-01 08:56:18,098 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:56] WARN - 
StepInstance 242 is being re-run following a failure.
2014-06-01 08:56:27,402 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:146] 
ERROR - Command line failed with exit code: 134
Command: bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 
-a 4 -d /home/macmanes/interproscan-5.4-47.0/data/pirsf/2.84/sf.seq -i 
/home/macmanes/interproscan-5.4-47.0/temp/davinci_20140601_070135568_9iu4//jobPI
RSF-2.84
/000000000101_000000000150.blastInputFile.fasta
Error output from binary:
libgcc_s.so.1 must be installed for pthread_cancel to work

2014-06-01 08:56:27,402 
[uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] ERROR - 
Execution thrown when attempting to executeInTransaction the StepExecution.  
All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 134
Command: bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 
-a 4 -d /home/macmanes/interproscan-5.4-47.0/data/pirsf/2.84/sf.seq -i 
/home/macmanes/interproscan-5.4-47.0/temp/davinci_20140601_070135568_9iu4//jobPI
RSF-2.84
/000000000101_000000000150.blastInputFile.fasta
Error output from binary:
libgcc_s.so.1 must be installed for pthread_cancel to work

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:148)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
    at sun.reflect.GeneratedMethodAccessor65.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:181)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Thread.java:744)
2014-06-01 08:56:27,685 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:56] WARN - 
StepInstance 331 is being re-run following a failure.
2014-06-01 08:56:41,970 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:146] 
ERROR - Command line failed with exit code: 134
Command: bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 
-a 4 -d /home/macmanes/interproscan-5.4-47.0/data/pirsf/2.84/sf.seq -i 
/home/macmanes/interproscan-5.4-47.0/temp/davinci_20140601_070135568_9iu4//jobPI
RSF-2.84
/000000000151_000000000200.blastInputFile.fasta
Error output from binary:
libgcc_s.so.1 must be installed for pthread_cancel to work

2014-06-01 08:56:41,971 
[uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] ERROR - 
Execution thrown when attempting to executeInTransaction the StepExecution.  
All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 134
Command: bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 
-a 4 -d /home/macmanes/interproscan-5.4-47.0/data/pirsf/2.84/sf.seq -i 
/home/macmanes/interproscan-5.4-47.0/temp/davinci_20140601_070135568_9iu4//jobPI
RSF-2.84
/000000000151_000000000200.blastInputFile.fasta
Error output from binary:
libgcc_s.so.1 must be installed for pthread_cancel to work

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:148)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
    at sun.reflect.GeneratedMethodAccessor65.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:181)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Thread.java:744)
2014-06-01 08:56:42,255 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:56] WARN - 
StepInstance 242 is being re-run following a failure.
2014-06-01 08:56:52,396 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:146] 
ERROR - Command line failed with exit code: 134
Command: bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 
-a 4 -d /home/macmanes/interproscan-5.4-47.0/data/pirsf/2.84/sf.seq -i 
/home/macmanes/interproscan-5.4-47.0/temp/davinci_20140601_070135568_9iu4//jobPI
RSF-2.84
/000000000101_000000000150.blastInputFile.fasta
Error output from binary:
libgcc_s.so.1 must be installed for pthread_cancel to work

2014-06-01 08:56:52,397 
[uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] ERROR - 
Execution thrown when attempting to executeInTransaction the StepExecution.  
All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 134
Command: bin/blast/2.2.6/blastall -p blastp -F F -e 0.0005 -b 300 -v 300 -m 8 
-a 4 -d /home/macmanes/interproscan-5.4-47.0/data/pirsf/2.84/sf.seq -i 
/home/macmanes/interproscan-5.4-47.0/temp/davinci_20140601_070135568_9iu4//jobPI
RSF-2.84
/000000000101_000000000150.blastInputFile.fasta
Error output from binary:
libgcc_s.so.1 must be installed for pthread_cancel to work

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:148)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
    at sun.reflect.GeneratedMethodAccessor65.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:181)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Thread.java:744)
2014-06-01 08:56:52,983 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL 
- Analysis step 331 : Run BLAST binary for PIRSF for proteins 101 to 150 has 
failed irretrievably.  Available StackTraces follow.
2014-06-01 08:56:52,984 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL 
- The JVM will now exit with a non-zero exit status.
2014-06-01 08:56:52,984 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:105] ERROR - 
Exception thrown by StandaloneBlackBoxMaster:
java.lang.IllegalStateException: InterProScan exiting with non-zero status, see 
logs for further information.
    at uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError.failed(NonZeroExitOnUnrecoverableError.java:42)
    at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:47)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. 
Check the log file for details

Original issue reported on code.google.com by [email protected] on 1 Jun 2014 at 1:12

[interhelp #25063] Missing the 6th field (Signature Description) in tsv output for SUPERFAMILY

What steps will reproduce the problem?
1. run the interpro
2. check the 6th field for SUPERFAMILY hits
3. The value is missing (you can see it in XML output)

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


What version of the product are you using? On what operating system?

Interproscan 5 on LINUX 

Please provide any additional information below.

Here is the description from your project home about TSV format

The TSV format presents the match data in columns as follows:

    Protein Accession (e.g. P51587)
    Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
    Sequence Length (e.g. 3418)
    Analysis (e.g. Pfam / PRINTS / Gene3D)
    Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
    Signature Description (e.g. BRCA2 repeat profile)
    Start location
    Stop location
    Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
    Status - is the status of the match (T: true)
    Date - is the date of the run
    (InterPro annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
    (InterPro annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
    (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
    (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)

Original issue reported on code.google.com by [email protected] on 7 Aug 2014 at 6:36

Feature request: accept stdin

Hi guys

In order to facilitate our mpi jobs:
Would it be possible to allow interproscan.sh accept STDIN and write to STDOUT 
(for single file format e.g. -o -)? I guess it would still write the STDIN as a 
temporary fasta file (like it does with normal input).

For single file format I guess we can use the XML to produce any of the other 
formats ?
(is there a protocol for that?)

many thanks
alexie

Original issue reported on code.google.com by [email protected] on 11 Feb 2013 at 12:15

Delivered pfscan-binary is linked to outdated library libg2c.so.0

What steps will reproduce the problem?
1. On latest Debian and Ubuntu >= 10.04 running standalone Interproscan-5 with 
options: -F TSV -goterms -iprlookup -pa on a query protein produces the 
following error:

java -Xmx2g -jar interproscan-5.jar -F TSV -goterms -iprlookup -pa -i 
test_1_prot.fasta test_1_prot_iprscan_out.tsv

Welcome to InterProScan v5.
Running InterProScan v5 in STANDALONE mode...
2012-05-15 12:02:28,028 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:123] 
ERROR - Command line failed with exit code: 141
Command: bin/ps_scan.pl -d data/prosite/20.66/prosite.dat --pfscan bin/pfscan 
-s -m -o gff 
temp/dell-node-4.mpipz.mpg.de_20120515_120040054_154q/jobPrositeProfiles/0000000
00001_000000000001.fasta
Error output from binary:
bin/pfscan: error while loading shared libraries: libg2c.so.0: cannot open 
shared object file: No such file or directory

2012-05-15 12:02:28,032 
[uk.ac.ebi.interpro.scan.jms.activemq.AmqInterProScanWorker:100] ERROR - 
Execution thrown when attempting to executeInTransaction the StepExecution.  
All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 141
Command: bin/ps_scan.pl -d data/prosite/20.66/prosite.dat --pfscan bin/pfscan 
-s -m -o gff 
temp/dell-node-4.mpipz.mpg.de_20120515_120040054_154q/jobPrositeProfiles/0000000
00001_000000000001.fasta
Error output from binary:
bin/pfscan: error while loading shared libraries: libg2c.so.0: cannot open 
shared object file: No such file or directory

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:125)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:83)
    at sun.reflect.GeneratedMethodAccessor54.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:309)
    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 $Proxy78.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.AmqInterProScanWorker.onMessage(AmqInterProScanWorker.java:96)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:560)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:498)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:467)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:325)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:263)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1058)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1050)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:947)
    at java.lang.Thread.run(Thread.java:662)
2012-05-15 12:02:28,266 
[uk.ac.ebi.interpro.scan.jms.activemq.AmqInterProScanMaster:163] WARN - 
StepInstance 4 is being re-run following a failure.

The input fasta file looks like this:
cat test_1_prot.fasta 
>Protein 1
MEGVQVTSRVSSPKATGLWKPGYDCRLTGLWNPSMCLAAAFSACARVCQARGRISSDWMV
LNNVSSRLRRKSVAQDVQRGAFFTPAIFLAEVSDRCSCRAEIGLILGRPGKSLAVRTHLA
PIAA

The cause of this is an outdated binary of pfscan:
ldd bin/pfscan 
    linux-vdso.so.1 =>  (0x00007fff0fdff000)
    libg2c.so.0 => not found
    libm.so.6 => /lib/libm.so.6 (0x00007f3115c98000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f3115a82000)
    libc.so.6 => /lib/libc.so.6 (0x00007f3115721000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f3115f2c000)

libg2c.so.0 depends on GCC 3.4, not the current 4.x

Downloading pftools source and compiling them manually runs fine and links as 
follows:
ldd bin/pfscan
    linux-vdso.so.1 =>  (0x00007fff15090000)
    libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f1e0dc44000)
    libm.so.6 => /lib/libm.so.6 (0x00007f1e0d9c1000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f1e0d7ab000)
    libc.so.6 => /lib/libc.so.6 (0x00007f1e0d44a000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f1e0df41000)

Please rebuild the binaries of pftools using the latest libraries, e.g. on a 
current version of Debian or Ubuntu!

Kind regards!

Original issue reported on code.google.com by [email protected] on 15 May 2012 at 2:42

Working or tmp directory and runtime switch or options

I am deploying InterProScan on a fileserver (readonly access).
I want output data or tmp files to be close to compute nodes.
I would like to be set at runtime, not at install time,
the place where temp files and results will
Is there a switch to allow this ?
Thanks
Alain

Original issue reported on code.google.com by [email protected] on 12 Jan 2012 at 9:39

Attempting to create a Gene3D match that has no alignment data

This is what I try:
> interproscan.sh -i test.fa -f tsv --goterms --pathways
Welcome to InterProScan 5RC4
Running the following analyses:
[jobProDom-2006.1, jobPanther-7.2, jobGene3d-3.3.0, jobSMART-6.2, 
jobTIGRFAM-12.0, jobPfamA-26.0, jobSuperFamily-1.75, jobPrositePatterns-20.83, 
jobPRINTS-42.0, jobPIRSF-2.82, jobPrositeProfiles-20.83, jobHAMAP-201207.04, 
jobCoils-2.2]
Running InterProScan v5 in STANDALONE mode...

with this java:
java version "1.7.0_13"
Java(TM) SE Runtime Environment (build 1.7.0_13-b20)
Java HotSpot(TM) 64-Bit Server VM (build 23.7-b01, mixed mode)

After some seconds it crashes with the following stacktrace:

java.lang.IllegalStateException: Attempting to create a Gene3D match that has 
no alignment data.
    at uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Gene3DHmmer3ParserSupport.createMatch(Gene3DHmmer3ParserSupport.java:32)
    at uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Gene3DHmmer3ParserSupport.createMatch(Gene3DHmmer3ParserSupport.java:16)
    at uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.AbstractHmmer3ParserSupport.addMatch(AbstractHmmer3ParserSupport.java:85)
    at uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Gene3DHmmer3ParserSupport.addMatch(Gene3DHmmer3ParserSupport.java:16)
    at uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Hmmer3SearchMatchParser.parse(Hmmer3SearchMatchParser.java:183)
    at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:66)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:84)
    at sun.reflect.GeneratedMethodAccessor64.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:601)
    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 sun.proxy.$Proxy94.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)

Is there any workaround to make interproscan to ignore the error and continue 
with the next sequence? Or can I prefilter my sequences to work around the 
problem?

Original issue reported on code.google.com by [email protected] on 19 Feb 2013 at 9:21

Attachments:

test.fa

tsv output of ver5 is not compatible with ver4

What steps will reproduce the problem?
1. run both instances (4.8 and 5RC1) of iprscan with output format 'tsv' and 
ask for goterms.

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

example of expected output:
orf00004_892-3075_-1_2181   00CB64BAA0249C13    727 HMMPfam PF00403 HMA 15  65  5.7e-13
    T   02-Jul-2012 IPR006121   Heavy metal-associated domain, HMA  Biological Process: 
metal ion transport (GO:0030001), Molecular Function: metal ion binding 
(GO:0046872)

output we get:
orf00004_892-3075_-1_2181   346cdeb0fd70c925b4586322dd709bf6    727 Pfam    PF00403 Heav
y-metal-associated domain   15  65  5.7E-13 T   04-07-2012  IPR006121   Heavy 
metal-associated domain, HMA    GO:0030001|GO:0046872


What version of the product are you using? On what operating system?
current RC1 on Linux rserv01.vital-it.ch 2.6.32-220.17.1.el6.x86_64 #1 SMP Wed 
May 16 00:01:37 BST 2012 x86_64 x86_64 x86_64 GNU/Linux

Please provide any additional information below.

Would you have a ipr5->4 converter or any option to force ipr4 output?
Thanks

Laurent Falquet
[email protected]

Original issue reported on code.google.com by [email protected] on 4 Jul 2012 at 11:06

Feature request: report query sequences with no-hits in output

What steps will reproduce the problem?
1. Ran standalone interproscan on multi-fasta amino acid file.
2. Job was terminated by computer cluster due to time constraints.
3. From tsv output it is impossible to tell which query sequences tried and 
failed. Query sequence do not appear in tsv file in same order as in fasta file.

Please consider adding an option where query sequences whose search completed 
and resulted in no-hits are reported as such. 

Thank you!

Original issue reported on code.google.com by [email protected] on 15 Feb 2013 at 1:57

libssl.so.10 missing

What steps will reproduce the problem?
1. try to search a nucleotide fasta
2. export to GFF3
3.

What is the expected output? What do you see instead?
The program gives me an error

What version of the product are you using? On what operating system?
INterproscan rc1 or 2 under centos

Please provide any additional information below.
with protein sequences it runs smoothly

Original issue reported on code.google.com by brandao.marcelo on 17 Jul 2012 at 6:02

problem with ncoils

What steps will reproduce the problem?
1.  all my runs produce a problem
2.
3.

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

I get an error

java.lang.IllegalStateException: IOException thrown when attempting to run 
binary
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:108)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:82)
        at sun.reflect.GeneratedMethodAccessor66.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:318)
        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 $Proxy90.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.activemq.AmqInterProScanWorker.onMessage(AmqInterProScanWorker.java:96)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:561)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:499)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:467)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:325)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:263)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1059)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1051)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:948)
        at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, 
No such file or directory
        at java.lang.ProcessBuilder.start(Unknown Source)
        at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:102)
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:106)
        ... 21 more
Caused by: java.io.IOException: error=2, No such file or directory
        at java.lang.UNIXProcess.forkAndExec(Native Method)
        at java.lang.UNIXProcess.<init>(Unknown Source)
        at java.lang.ProcessImpl.start(Unknown Source)
        ... 24 more


What version of the product are you using? On what operating system?
interproscan5 and the operating sistem is ubuntu 64 bit

Please provide any additional information below.

I think that the problem is the ncoils software which is not able to run. I 
tested to run the software from the londer where the software is located in 
/programs/interproscan5/interproscan-5-RC1/bin/coils and it gives this error 
too: ./ncoils: No such file or directory

hope that you can help.

thanks

Original issue reported on code.google.com by [email protected] on 9 Jun 2012 at 1:40

[interhelp #25609] InterProScan 5.6-48.0 doesn't return any InterPro annotation for PIRSF matches

It does not annotate PIRSF matches with InterPro entries and associated 
cross-references like pathway or GO information.

Original issue reported on code.google.com by [email protected] on 15 Aug 2014 at 8:49

Hanging master under certain circumstances in CLUSTER mode

Under certain circumstances it is possible that !InterProScan is hanging. This 
will only happen in CLUSTER mode. You will notice on the farm that the master 
application is running meanwhile all workers had shut down.

One way to avoid the happening of such circumstances is to increase the time of 
the following parameter in your properties file:
*jvm.maximum.idle.time.seconds*=300

Original issue reported on code.google.com by [email protected] on 21 Jan 2014 at 12:01

[interhelp #24091] libmysqlclient.so.16: cannot open shared object file: No such file or directory

Hi team,

It looks like interproscan can't find this .so file while it's actually on my 
system, located here:

[04:02] ~/interproscan/src/interproscan-5.4-47.0 ⇒ locate libmysqlclient.so.16
/usr/lib64/mysql/libmysqlclient.so.16

Can you please let me know how to fix this ?

Thanks
Seb

More details:

What steps will reproduce the problem?
1. execute interproscan.sh not in cluster mode.
2. input is a DNA file
3. --goterms and --iprlookup activated

What is the expected output? What do you see instead?
interproscan results I suppose.

Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: 
libmysqlclient.so.16: cannot open shared object file: No such file or directory


What version of the product are you using? On what operating system?
v5.4-47 on a debian

Please provide any additional information below.

Command line:
./interproscan.sh -d ~/interproscan/output/ -f tsv --goterms --iprlookup -t n 
-i chunk_10.fa


Output:
23/07/2014 03:32:26:769 Welcome to InterProScan-5.4-47.0
23/07/2014 03:32:38:496 Running the following analyses:
[jobTIGRFAM-13.0, jobProDom-2006.1, jobPIRSF-2.84, jobPfamA-27.0, 
jobPrositeProfiles-20.97, jobSMART-6.2, jobHAMAP-201311.27, 
jobPrositePatterns-20.97, jobPRINTS-42.0, jobSuperFamily-1.75, jobCoils-2.2, 
jobGene3d-3.5.0]
23/07/2014 03:32:38:527 Running InterProScan v5 in STANDALONE mode...
2014-07-23 03:32:45,160 
[uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:146] 
ERROR - Command line failed with exit code: 127
Command: bin/nucleotide/getorf -sf pearson -sequence 
~/interproscan/src/interproscan-5.4-47.0/chunk_10.fa -outseq 
~/interproscan/src/interproscan-5.4-47.0/temp/XXXXXX/jobLoadNucleicAcidSequence/
orfs.fasta -minsize 50
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: 
libmysqlclient.so.16: cannot open shared object file: No such file or directory

2014-07-23 03:32:45,164 
[uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:193] ERROR - 
Execution thrown when attempting to executeInTransaction the StepExecution.  
All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 127
Command: bin/nucleotide/getorf -sf pearson -sequence 
~/interproscan/src/interproscan-5.4-47.0/chunk_10.fa -outseq 
~/interproscan/src/interproscan-5.4-47.0/temp/XXXXXX/jobLoadNucleicAcidSequence/
orfs.fasta -minsize 50
Error output from binary:
bin/nucleotide/getorf: error while loading shared libraries: 
libmysqlclient.so.16: cannot open shared object file: No such file or directory

        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:148)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        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 $Proxy94.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:181)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Thread.java:662)

Original issue reported on code.google.com by [email protected] on 23 Jul 2014 at 8:13

Schema / DTD of XML output

Hello,

I'm looking for a DTD or XML Schema for helping me parse Interproscan 5 XML 
output format. Is it provided anywhere?

Thanks!

Original issue reported on code.google.com by [email protected] on 19 Apr 2013 at 1:31

working directory as a job option

My name is Shengqiang Shu, working with David Goodstein in JGI.

I have not found an option to pass in the working directory for a job. The 
reason is that NFS is slow and I want to use the farm node local disk as 
temporary working directory instead of 'configured working directory'.

If this option is not implemented, can we expect this will be implemented?

Thanks.


S. Shu

Original issue reported on code.google.com by [email protected] on 14 Sep 2011 at 10:11

Installation/running problem

What steps will reproduce the problem?
1. Installation problem or running interproscan.sh

What is the expected output? What do you see instead?
I want to run InterProScan stand-alone in my computer

What version of the product are you using? On what operating system?
InterProScan 5 v44.0

Please provide any additional information below.

I have done the following steps to install and use the program: 

# Installation and unpacking InterProScan 5 v44.0

mkdir my_interproscan
cd my_interproscan
wget 
ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5-44.0/interproscan-5-44.0-64-bi
t.tar.gz
tar -pxvzf interproscan-5-44.0-64-bit.tar.gz

# Run GO terms search
./interproscan.sh –i iputfile.fasta –f tsv –t n –dp –goterms –o 
outputfile

I have just done the steps that I show you. When I run the last script I have 
obtained "permisson denied to interproscan.sh". So I have used:

chmod +x interproscan.sh

But when I run again I obtain the following text:

./interproscan.sh -i test_proteins.fasta -f tsv 

08/10/2013 16:40:15:830 Welcome to InterProScan-5-44.0
./interproscan.sh: line 38:  6814 Killed                  "$JAVA" 
-XX:+UseParallelGC -XX:ParallelGCThreads=2 -XX:+AggressiveOpts 
-XX:+UseFastAccessorMethods -Xms128M -Xmx2048M -jar interproscan-5.jar $@ -u 
$USER_DIR

I am not a expert in command-line, but I would like to run a InterProScan 
search to obtain GO terms for a large fasta file (RNA-seq data). Thank you in 
advance.

Original issue reported on code.google.com by [email protected] on 8 Oct 2013 at 2:50

Provide functionality which allows to override the location of the interproscan.properties file

Has been requested multiple times.

Original issue reported on code.google.com by [email protected] on 8 Jul 2014 at 9:03

Support authenticated proxy servers

At the moment proxy servers requiring authentication are not supported.

Original issue reported on code.google.com by [email protected] on 18 Mar 2014 at 1:03

Convert mode fails

*Which version of InterProScan 5?*
5RC7

*How to reproduce?*
Run InterProScan 5RC7 in convert mode fails on some XML files created with 
version 5RC7.

*Command:*
interproscan.sh -mode convert -f gff3 -i inputFile-5RC6.xml -b 
outputFile-5RC6.gff3

Original issue reported on code.google.com by [email protected] on 14 Aug 2013 at 8:49

Code review request

Branch name:

Purpose of code changes on this branch:

Testing the code review request


When reviewing my code changes, please focus on:

Whether this request system works


After the review, I'll merge this branch into:
/trunk

Original issue reported on code.google.com by [email protected] on 10 Oct 2012 at 2:02

[jobPfamA-26.0] fails

What steps will reproduce the problem?
1. Run interproscan.sh -aapl PfamA some.seq
2.
3.

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


13/05/2013 14:21:11 Welcome to InterProScan 5RC6
Running the following analyses:
[jobPfamA-26.0]
Running InterProScan v5 in STANDALONE mode...
Pre-calculated match lookup service DISABLED.  Please wait for match 
calculations to complete...
13/05/2013 14:22:36 38% completed
2013-05-13 14:22:42,359 
[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: IOException thrown when attempting to parse 
temp/iq218_20130513_142132149_i72k/jobPfamA-26.0/000000000001_000000000004.raw.o
ut
    at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:77)
    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(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    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 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(Thread.java:679)
Caused by: java.io.IOException: No locks available
    at sun.nio.ch.FileChannelImpl.lock0(Native Method)
    at sun.nio.ch.FileChannelImpl.lock(FileChannelImpl.java:887)
    at uk.ac.ebi.interpro.scan.io.model.GaValuesRetriever.loadMappingFromPropertiesFile(GaValuesRetriever.java:141)
    at uk.ac.ebi.interpro.scan.io.model.GaValuesRetriever.lazyInitialise(GaValuesRetriever.java:95)
    at uk.ac.ebi.interpro.scan.io.model.GaValuesRetriever.getSequenceGAForAccession(GaValuesRetriever.java:75)
    at uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Pfam_A_Hmmer3Hmmer3ParserSupport.addMatch(Pfam_A_Hmmer3Hmmer3ParserSupport.java:96)
    at uk.ac.ebi.interpro.scan.io.match.hmmer.hmmer3.Hmmer3SearchMatchParser.parse(Hmmer3SearchMatchParser.java:183)
    at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:66)
    ... 22 more
What version of the product are you using? On what operating system?

this is RC6 and is running on a Sun Grid Engine machine 

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 13 May 2013 at 9:44

Anotation of a sequence of nucleic acid

What steps will reproduce the problem?
1. I need do an anotation for nucleic acid
2. Running interproscan 5 
3. I use the next comand:  ./interproscan.sh -t n -i contigs.fa -f GFF3 -o 
contigs.fa.GFF3  

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

Welcome to InterProScan 5RC4
Running the following analyses:
[jobProDom-2006.1, jobPanther-7.2, jobGene3d-3.3.0, jobSMART-6.2, 
jobTIGRFAM-12.0, jobPfamA-26.0, jobSuperFamily-1.75, jobPrositePatterns-20.83, 
jobPRINTS-42.0, jobPIRSF-2.82, jobPrositeProfiles-20.83, jobHAMAP-201207.04, 
jobCoils-2.2]
Running InterProScan v5 in STANDALONE mode...
Available matches will be retrieved from the pre-calculated match lookup 
service.

Matches for any sequences that are not represented in the lookup service will 
be calculated locally.
2013-01-11 13:17:28,592 
[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: Couldn't find nucleotide sequence by the 
following cross reference: NODE_11386_length_690_cov_9
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.createAndPersistNewORFs(ProteinLoader.java:293)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.persistBatch(ProteinLoader.java:182)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.addProteinToBatch(ProteinLoader.java:162)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.lookupProteins(ProteinLoader.java:140)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.storeAll(ProteinLoader.java:254)
    at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:104)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    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 $Proxy90.loadSequences(Unknown Source)
    at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep.execute(FastaFileLoadStep.java:151)
    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(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    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 $Proxy94.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Thread.java:679)
2013-01-11 13:17:28,771 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:44] WARN - 
StepInstance 2 is being re-run following a failure.
Available matches will be retrieved from the pre-calculated match lookup 
service.

Matches for any sequences that are not represented in the lookup service will 
be calculated locally.
2013-01-11 13:51:52,836 
[uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener:106] ERROR - Execution 
thrown when attempting to executeInTransaction the StepExecution.  All database 
activity rolled back.
javax.persistence.PersistenceException: 
org.hibernate.PersistentObjectException: detached entity passed to persist: 
uk.ac.ebi.interpro.scan.model.Protein
    at org.hibernate.ejb.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1214)
    at org.hibernate.ejb.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1147)
    at org.hibernate.ejb.AbstractEntityManagerImpl.convert(AbstractEntityManagerImpl.java:1153)
    at org.hibernate.ejb.AbstractEntityManagerImpl.persist(AbstractEntityManagerImpl.java:678)
    at sun.reflect.GeneratedMethodAccessor46.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    at org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:240)
    at $Proxy41.persist(Unknown Source)
    at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insertNewProteins(ProteinDAOImpl.java:253)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    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 $Proxy42.insertNewProteins(Unknown Source)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.persistBatch(ProteinLoader.java:178)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.addProteinToBatch(ProteinLoader.java:162)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.lookupProteins(ProteinLoader.java:140)
    at uk.ac.ebi.interpro.scan.business.sequence.ProteinLoader.storeAll(ProteinLoader.java:254)
    at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:104)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    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 $Proxy90.loadSequences(Unknown Source)
    at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep.execute(FastaFileLoadStep.java:151)
    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(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    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 $Proxy94.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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(Thread.java:679)
Caused by: org.hibernate.PersistentObjectException: detached entity passed to 
persist: uk.ac.ebi.interpro.scan.model.Protein
    at org.hibernate.event.def.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:127)
    at org.hibernate.event.def.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:61)
    at org.hibernate.impl.SessionImpl.firePersist(SessionImpl.java:808)
    at org.hibernate.impl.SessionImpl.persist(SessionImpl.java:782)
    at org.hibernate.impl.SessionImpl.persist(SessionImpl.java:786)
    at org.hibernate.ejb.AbstractEntityManagerImpl.persist(AbstractEntityManagerImpl.java:672)
    ... 56 more
2013-01-11 13:51:52,892 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL 
- Analysis step 2 : Load proteins from a fasta file generated by GetOrf and 
create required JobInstance objects.  Also creates OpenReadingFrame records to 
connect the proteins to the NucleicAcid records. for proteins null to null has 
failed irretrievably.  Available StackTraces follow.
2013-01-11 13:51:52,892 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL 
- The JVM will now exit with a non-zero exit status.

What version of the product are you using? On what operating system?

Interproscan 5. Ubuntu 12.04
Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 14 Jan 2013 at 2:18

InterProScan 5RC6 with -appl Coils executeInTransaction error

What steps will reproduce the problem?
1.
./interproscan.sh -appl Coils -i test_proteins.fasta -f tsv

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

24/06/2013 12:28:52 Welcome to InterProScan 5RC6
Running the following analyses:
[jobCoils-2.2]
Running InterProScan v5 in STANDALONE mode...
Available matches will be retrieved from the pre-calculated match lookup 
service.

Matches for any sequences that are not represented in the lookup service will 
be calculated locally.
2013-06-24 12:29:52,424 
[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: IOException thrown when attempting to run 
binary
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:108)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, 
No such file or directory
    at java.lang.ProcessBuilder.start(Unknown Source)
    at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:102)
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:106)
    ... 22 more
Caused by: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.<init>(Unknown Source)
    at java.lang.ProcessImpl.start(Unknown Source)
    ... 25 more
24/06/2013 12:29:52 29% completed
2013-06-24 12:29:52,786 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:48] WARN - 
StepInstance 3 is being re-run following a failure.
2013-06-24 12:29:52,816 
[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: IOException thrown when attempting to run 
binary
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:108)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, 
No such file or directory
    at java.lang.ProcessBuilder.start(Unknown Source)
    at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:102)
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:106)
    ... 22 more
Caused by: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.<init>(Unknown Source)
    at java.lang.ProcessImpl.start(Unknown Source)
    ... 25 more
2013-06-24 12:29:53,176 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:48] WARN - 
StepInstance 3 is being re-run following a failure.
2013-06-24 12:29:53,204 
[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: IOException thrown when attempting to run 
binary
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:108)
    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.$Proxy95.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.activemq.WorkerListener.onMessage(WorkerListener.java:102)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, 
No such file or directory
    at java.lang.ProcessBuilder.start(Unknown Source)
    at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:102)
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:106)
    ... 22 more
Caused by: java.io.IOException: error=2, No such file or directory
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.<init>(Unknown Source)
    at java.lang.ProcessImpl.start(Unknown Source)
    ... 25 more
2013-06-24 12:29:53,554 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL 
- Analysis step 3 : Run fingerprintscan Binary for selected proteins for 
proteins 1 to 4 has failed irretrievably.  Available StackTraces follow.
2013-06-24 12:29:53,559 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL 
- The JVM will now exit with a non-zero exit status.

What version of the product are you using? On what operating system?
InterProScan 5RC6 on Ubuntu 12.04.1 LTS - x64
java version "1.7.0_25"

I don't know if I'm doing anything wrong, but I've tested -appl 
TIGRFAM,PIRSF,ProDom,Panther,SMART,PrositeProfiles,HAMAP,PfamA,PrositePatterns,P
RINTS,SuperFamily,Gene3d and they all worked fine.

Thanks!

Original issue reported on code.google.com by [email protected] on 24 Jun 2013 at 12:47

[interhelp #26350] problems running interproscan in clustermode on SGE cluster

What steps will reproduce the problem?
1. interproscan.sh -dp -f TSV -goterms -iprlookup -pa -i test_proteins.fasta 
-mode cluster -clusterrunid testIPR


What is the expected output? What do you see instead?
I don't get any interpro results back. All I get in the .out and .err file of 
the submitted "i5t1master" jobs are message about connection problems. (see 
files attached, replaced servername by "submission_hostname").

What version of the product are you using? On what operating system?
interproscan5-7-48
linux RedHat Enterprise Version

Please provide any additional information below.
As far as I can see, the interproscan.sh script submits 2 jobs to our cluster 
(i5t1master), but apart from the messages in the attached files they don't do 
anything. After a while they stop/die and the main interproscan.sh script hangs 
forever.

Many thanks in advance,
lieven

Original issue reported on code.google.com by [email protected] on 28 Aug 2014 at 4:18

Attachments:

Proxy setup fails

What steps will reproduce the problem?

1.) Entered configuration details in interproscan.properties:
precalculated.match.lookup.service.proxy.host=<some internal host>
precalculated.match.lookup.service.proxy.port=8080

2.) Run InterProScan with that configuration

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

Matches for any sequences that are not represented in the lookup service will 
be calculated locally.
2014-01-17 10:28:02,942 
[uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:21
4] WARN -

The following problem was encountered by the pre-calculated match lookup 
service:
www.ebi.ac.uk
Pre-calculated match lookup service failed - analysis proceeding to run locally

============================================================
The pre-calculated match lookup service has been configuredin the 
interproscan.properties file. Unfortunately the web service has failed. Check 
the configuration of this service in the interproscan.properties file and, if 
nessary, set the following property to look like this:
precalculated.match.lookup.service.url=

If the problem persists, check if this is a firewall or proxy issue.
If it is a proxy issue, then setting the following property in the 
interproscan.properties file should work:
precalculated.match.lookup.service.proxy.host=
precalculated.match.lookup.service.proxy.port=

If this still does not work please inform the InterPro team of this error by 
sending an email to:
[email protected]

In the meantime, the analysis will continue to run locally.
==============================

Original issue reported on code.google.com by [email protected] on 17 Jan 2014 at 12:22

[interhelp #14905] Running on LSF-like cluster

Hi,

I've ben trying to run Interproscan on an LSF-like cluster, specifically on 
OpenLava. Openlava (openlava.org) is a fork of the defunct Platform Lava and 
Platform LSF and is, at least for my purpose so far, syntax-compatible with LSF.

However, when trying to run Interproscan, I get this:

[uk.ac.ebi.interpro.scan.jms.master.DistributedBlackBoxMaster:299] WARN - 
Restarted scheduledExecutorService for updating ClusterState

Works fine if I run it on a single machine tho. Any ideas what sort of problem 
I could be looking at here?

Cheers,

Marc

Original issue reported on code.google.com by [email protected] on 18 Feb 2014 at 2:16

results written to install directory

What steps will reproduce the problem?
1. Run interproscan.sh from different directory (e.g. user's home)
2. Use default or relative basename
3.

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

Expected: results will be written to same directory as input file
Observed: results are written to install directory (same dir as interproscan.sh)


What version of the product are you using? On what operating system?

interproscan 5RC1 64-bit
Debian 6.0


Please provide any additional information below.

By default or when giving relative names to '-b', the results are written to 
the same directory as interproscan.sh. This is unexpected and problematic when 
users do not have write permissions on this directory tree. The workaround is 
to give '-b' an absolute pathname to the desired output directory, but this 
seems like a bug in the software.

Thanks.

Original issue reported on code.google.com by [email protected] on 6 Jun 2012 at 4:45

[deleted issue]

[deleted issue]

[interhelp #22797] interproscan.sh problem

Dear Interproscan-5.4-47.0 developers

I downloaded “Interproscan-5.4-47.0” (64 bit distribution) and its checksum 
give OK message.Unfortunately,to verify if Interproscan-5.4-47.0 software is 
installed correctly or not, I run interproscan.sh with no arguments I got error 
message below;

vahap@bio[Interproscan-5.4-47.0] sh interproscan.sh
interproscan.sh: 17: interproscan.sh: [[: not found
interproscan.sh: 29: interproscan.sh: [[: not found
interproscan.sh: 38: interproscan.sh: [[: not found
java is /usr/bin/java: not found

I think that  I just need a help to show me how to setup java path in this 
script ?

Note: I checked that java is properly installed on my system. (in 
/usr/local/bin)

Thank you for your consideration in advance

-vahap eldem-

Original issue reported on code.google.com by [email protected] on 30 Jun 2014 at 9:56

downloading /installation issue

What steps will reproduce the problem?
1.Downloading a copy
2.Downloading from direct link
3.Check the copy using md5sum

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

1)Downloading a copy
wget 
ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.3-46.0/interproscan-5.3-46.0-6
4-bit.tar.gz

ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.3-46.0/interproscan-5.3-46.0-6
4-bit.tar.gz

  (try: 4) => `interproscan-5.3-46.0-64-bit.tar.gz'
Connecting to 192.168.2.251:3128... connected.
Logging in as anonymous ... 
Error in server response, closing control connection.
Retrying.

2) Downloaded from the direct link
This link does not work:
ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.3-46.0/interproscan-5.3-46.0-6
4-bit.tar.gz

What version of the product are you using? On what operating system?
No version trying retrieve a version and to install the software

Please provide any additional information below.

uname -a
Linux LEI13-0007U 3.5.0-34-generic #55~precise1-Ubuntu SMP Fri Jun 7 16:25:50 
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

java -version
java version "1.7.0_51"
Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)

perl -version
This is perl 5, version 14, subversion 2 (v5.14.2) built for 
x86_64-linux-gnu-thread-multi
(with 57 registered patches, see perl -V for more detail)

I am not a expert in command-line, but I would like to run a InterProScan 
search. Thank you in advance.

Original issue reported on code.google.com by [email protected] on 1 May 2014 at 8:40

FingerPrint match evalues appear to be incorrectly allocated for filtered results

Taking the Swiss-Prot sequence P51493 as an example, the FPScan binary gives 
maches to the following fingerprints at the E-values indicated:

INTRLEUKIN1B  (PR01359)   3.130760e-118
INTRLEUKN1AB  (PR01357)   1.463628e-49
INTERLEUKIN1  (PR00264)   7.086978e-22
IL1HBGF       (PR00262)   8.924590e-08

+ a match to INTRLEUKIN1X (PR01360), which will be/is being correctly filtered 
out by InterPro's hierarchy-based post-pocessing system.

Looking at the E-value output you sent me for the test set, the E-values for 
the individual models seem to be jumbled up. In fact, some models have 2 
different E-values, which is a definite indicator that something is going 
wrong! So, taking P51493 as an example again, we have:

PR00264 INTERLEUKIN1 1.5000000000000004E-49
PR00264 INTERLEUKIN1 8.90000000000001E-8
PR01359 INTRLEUKIN1B 1.5000000000000004E-49
PR00262 IL1HBGF 3.100000000000041E-118
PR01357 INTRLEUKN1AB 7.099999999999989E-22
PR01357 INTRLEUKN1AB 1.5000000000000004E-49
PR00262 IL1HBGF 1.5000000000000004E-49

Original issue reported on code.google.com by [email protected] on 12 Jul 2010 at 12:47

ncoils fails, kills interproscan on 64 bit fedora 20

What steps will reproduce the problem?
1. Download and uncompress interproscan-5.4-47.0-64-bit.tar.gz
2. ./interproscan.sh -i test_proteins.fasta -f tsv


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

Expect to see success. Instead get: InterProScan analysis failed. Exception 
thrown by StandaloneBlackBoxMaster. Check the log file for details

I have attached the error output.

What version of the product are you using? On what operating system?
5.4-47.0-64-bit, on Linux hemera.cesb.uky.edu 3.14.4-200.fc20.x86_64 #1 SMP Tue 
May 13 13:51:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

Please provide any additional information below.

The error appears to be from ncoils not being able to run, because it is a 32 
bit binary and I am on a 64 bit system.

Original issue reported on code.google.com by [email protected] on 30 May 2014 at 3:28

Attachments:

testLog.txt

Acces denied to dabases - test run

What steps will reproduce the problem?
1. Installing interproscan not in home directory in opensuse 12.3 on 64bit 
system
2. Running test procedure "./interproscan.sh -i test_proteins.fasta -f tsv"
from interproscan directory

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

I wanted to test if wverything is ok

What version of the product are you using? On what operating system?

interproscan 5RC6 on opensuse 12.3 64bit
with java version "1.7.0_21"
OpenJDK Runtime Environment (IcedTea 2.3.9) (suse-8.14.5-x86_64)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)

Please provide any additional information below.

Smetimes I have problems with permissions when I run program not from home 
directory.
"brak dostepu" in code means "acces denied"

zea@ip094183:/run/media/zea/dane2/my_interproscan/interproscan-5-RC6> sh 
./interproscan.sh -i test_proteins.fasta -f tsv
01/07/2013 14:37:58 Welcome to InterProScan 5RC6
Running the following analyses:
[jobTIGRFAM-13.0, jobProDom-2006.1, jobPanther-7.2, jobSMART-6.2, 
jobPrositeProfiles-20.89, jobPrositePatterns-20.89, jobPfamA-26.0, 
jobSuperFamily-1.75, jobPRINTS-42.0, jobGene3d-3.5.0, jobPIRSF-2.83, 
jobHAMAP-201302.26, jobCoils-2.2]
Running InterProScan v5 in STANDALONE mode...
Available matches will be retrieved from the pre-calculated match lookup 
service.

Matches for any sequences that are not represented in the lookup service will 
be calculated locally.
2013-07-01 14:38:15,883 
[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: IOException thrown when attempting to run 
binary
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:108)
    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(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:601)
    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(Thread.java:722)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": 
error=13, Brak dostępu
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1042)
    at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:102)
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:106)
    ... 22 more
Caused by: java.io.IOException: error=13, Brak dostępu
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:135)
    at java.lang.ProcessImpl.start(ProcessImpl.java:130)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1023)
    ... 24 more
01/07/2013 14:38:15 29% completed
2013-07-01 14:38:16,118 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:48] WARN - 
StepInstance 3 is being re-run following a failure.
2013-07-01 14:38:16,128 
[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: IOException thrown when attempting to run 
binary
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:108)
    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(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:601)
    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(Thread.java:722)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": 
error=13, Brak dostępu
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1042)
    at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:102)
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:106)
    ... 22 more
Caused by: java.io.IOException: error=13, Brak dostępu
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:135)
    at java.lang.ProcessImpl.start(ProcessImpl.java:130)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1023)
    ... 24 more
2013-07-01 14:38:16,358 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:48] WARN - 
StepInstance 3 is being re-run following a failure.
2013-07-01 14:38:16,366 
[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: IOException thrown when attempting to run 
binary
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:108)
    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(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:601)
    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(Thread.java:722)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": 
error=13, Brak dostępu
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1042)
    at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:102)
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:106)
    ... 22 more
Caused by: java.io.IOException: error=13, Brak dostępu
    at java.lang.UNIXProcess.forkAndExec(Native Method)
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:135)
    at java.lang.ProcessImpl.start(ProcessImpl.java:130)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:1023)
    ... 24 more
2013-07-01 14:38:16,599 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL 
- Analysis step 3 : Run fingerprintscan Binary for selected proteins for 
proteins 1 to 4 has failed irretrievably.  Available StackTraces follow.
2013-07-01 14:38:16,599 
[uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL 
- The JVM will now exit with a non-zero exit status.
zea@ip094183:/run/media/zea/dane2/my_interproscan/interproscan-5-RC6>

Original issue reported on code.google.com by [email protected] on 1 Jul 2013 at 12:49

[interhelp #25958] What cluster does it support? Only LSF?

I have a PBS cluster, and i hope it will support PBS soon

Original issue reported on code.google.com by [email protected] on 31 Mar 2013 at 1:36

[interhelp #23531] tmhmm interproscan.sh error

version:
InterProScan 5.4-47.0
tmhmm-2.0c

command:
interproscan.sh -i Chromosome_1_protein.fasta -f XML,GFF3

Error
/home/apps/scripts/tmhmm data/tmhmm/2.0/TMHMM2.0.model 
/home/data/fus_culmorum/036A_Manuscript_Fgraminearum_g                        
ome_reannotation/Chromosome-1_reannotation/publishable/temp/pear.rothamsted.ac.u
k_20140714_151840036_fpaz//jobTMHMM-2.0c/0                        
00000002989_000000003038.fasta -N 1 -PrintNumbers -background 0.081 0.015 0.054 
0.061 0.040 0.068 0.022 0.057 0.056 0.093                         0.025 0.045 
0.049 0.039 0.057 0.068 0.058 0.067 0.013 0.032
Option n is ambiguous (no-d, no-html, no-plot, no-short, no-v1, nod, nohtml, 
noplot, noshort, nov1)
Unknown option: printnumbers
Unknown option: background
Error on command line at /home/apps/scripts/tmhmm line 32.

Original issue reported on code.google.com by [email protected] on 14 Jul 2014 at 3:03

Convert mode misbehaves for nucleic acid sequences

What steps will reproduce the problem?
1. Run InterProScan in CONVERT mode against an XML input file, which contains 
nucleic acid sequence annotations
2. Specify GFF3 as output format
3. Here is the command:
./interproscan.sh -mode convert -i test_nt_seqs.fasta.xml -f gff3

What is the expected output?
##gff-version 3
##feature-ontology 
http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
##sequence-region reverse 1 384
reverse provided_by_user    nucleic_acid    1   384 .   +   .   Name=reverse;md5=51884b55e9f02
5009d1b4682889bab2c;ID=reverse
reverse getorf  ORF 1   384 .   +   .   Name=reverse_6;Target=pep_reverse_1_384 1 
128;md5=51884b55e9f025009d1b4682889bab2c;ID=orf_reverse_1_384
reverse getorf  polypeptide 1   128 .   +   .   md5=d1b6cbf29dde9e5220196f3f6114a1c3;ID=p
ep_reverse_1_384
reverse PRINTS  protein_match   78  87  .   +   .   Name=PR00003;signature_desc=4-disulphid
e core signature;Target=null 78 87;status=T;ID=match$1_78_87;date=20-09-2013
reverse PRINTS  protein_match   107 116 .   +   .   Name=PR00003;signature_desc=4-disulph
ide core signature;Target=null 107 
116;status=T;ID=match$1_107_116;date=20-09-2013

What do you see instead?
##gff-version 3
##feature-ontology 
http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
null    Pfam    protein_match   432 579 2.0E-68 +   .   Name=PF08144;signature_desc=CPL 
(NUC119) domain;Target=null 432 
579;status=T;ID=match$1_432_579;Ontology_term="GO:0003723";date=20-09-2013;Dbxre
f="InterPro:IPR012959"
null    Gene3D  protein_match   136 487 2.5E-65 +   .   Name=G3DSA:1.25.10.10;Target=null 
136 487;status=T;ID=match$2_136_487;date=20-09-2013;Dbxref="InterPro:IPR011989"
null    ProSiteProfiles protein_match   492 530 .   +   .   Name=PS50302;signature_desc=Pum
ilio RNA-binding repeat profile.;Target=null 492 
530;status=T;ID=match$3_492_530;Ontology_term="GO:0003723";date=20-09-2013;Dbxre
f="InterPro:IPR001313"
null    ProSiteProfiles protein_match   200 235 .   +   .   Name=PS50302;signature_desc=Pum
ilio RNA-binding repeat profile.;Target=null 200 
235;status=T;ID=match$3_200_235;Ontology_term="GO:0003723";date=20-09-2013;Dbxre
f="InterPro:IPR001313"

Original issue reported on code.google.com by [email protected] on 20 Sep 2013 at 10:58

Override properties defined in interproscan.properties when caling interproscan.sh

Hi,

we would like to use a centralized version of interproscan5 for multiple users. 
However, as users have slightly different requirements, they would need to 
provide different interproscan.properties. So is there a way to override the 
ones defined in the file by providing some additional argument when calling 
interproscan.sh? Or is there a way to tell IPS5 which properties file to use?

Thanks
Holger

Original issue reported on code.google.com by [email protected] on 18 Jul 2013 at 6:11

Black-box version of I5 needs to be able to look up pre-calculated results

The current black-box version of I5 makes a copy of an empty database (empty, 
apart from Signatures / models).  This works well but does not provide a 
mechanism for looking up pre-calculated matches.

Original issue reported on code.google.com by [email protected] on 12 Jul 2010 at 12:49

HTML output not working in CONVERT mode

What steps will reproduce the problem?
1. Running CONVERT mode with -f html

[kmkeati2@compute-3-9 ~]$ /home/apps/iprscan/iprscan-5.44/interproscan.sh -mode 
convert -f html -i /home/a-m/kmkeati2/test_proteins_convert_mode.xml -b 
/home/a-m/kmkeati2/ 
04/10/2013 13:51:54:293 Welcome to InterProScan-5-44.0
04/10/2013 13:52:02:234 Running InterProScan v5 in CONVERT mode...
2013-10-04 13:52:04,170 
[uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesH
TMLResultWriter:217] WARN - Couldn't create temp directory 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/P22298.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/Q97R95.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/A2YIW7.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/A2VDN9.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/A0B786.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
java.io.FileNotFoundException: 
/home/a-m/kmkeati2/temp/compute-3-9.local_20131004_135202235_cic7/Q1A5X6.html 
(Not a directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:212)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:165)
    at java.io.FileWriter.<init>(FileWriter.java:90)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:178)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.ProteinMatchesHTMLResultWriter.write(ProteinMatchesHTMLResultWriter.java:146)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:347)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
2013-10-04 13:52:12,761 [uk.ac.ebi.interpro.scan.jms.converter.Converter:258] 
ERROR - Cannot write or create result file!
java.io.IOException: This archives contains unclosed entries.
    at org.apache.commons.compress.archivers.tar.TarArchiveOutputStream.finish(TarArchiveOutputStream.java:135)
    at uk.ac.ebi.interpro.scan.management.model.implementations.writer.TarArchiveBuilder.buildTarArchive(TarArchiveBuilder.java:72)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.outputToHTML(Converter.java:351)
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:228)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)
Exception in thread "main" java.lang.NullPointerException
    at uk.ac.ebi.interpro.scan.jms.converter.Converter.run(Converter.java:267)
    at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:275)


What is the expected output? What do you see instead?
Would expect to have a HTML file that has the corresponding information from 
the input XML file. Running this command yields the file 
test_proteins_convert_mode.xml.html.tar.gz that cannot be processed by the 
command tar -zxvf. 


What version of the product are you using? On what operating system?
InterProScan 5 (version 5-44.0); RedHat Enterprise Linux 6

Linux biocluster.igb.illinois.edu 2.6.32-220.13.1.el6.x86_64 #1 SMP Tue Apr 17 
23:56:34 BST 2012 x86_64 x86_64 x86_64 GNU/Linux


Please provide any additional information below.
The cluster is set up with PBS TORQUE, not LSF or SGE.

Original issue reported on code.google.com by [email protected] on 4 Oct 2013 at 8:54

[interhelp #24581] temporary directory location not passed to distributed workers

What steps will reproduce the problem?
1. set temporary.file.directory in interproscan.properties to something other 
than temp/...
2. run in cluster mode and do not specify -T option. Use the default value
3.

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

Expect that the distributed workers use temp directory in 
temporary.file.directory. Instead it uses temp/


What version of the product are you using? On what operating system?
interproscan-5.4-47.0 on debian 6.0.6 with SGE

Please provide any additional information below.

Original issue reported on code.google.com by [email protected] on 1 Aug 2014 at 6:35

PIRSF fails

When I try to run the PIRSF algorithm on out SGE cluster, I get some java error 
caused by 

Caused by: java.io.IOException: java.io.IOException: error=2, No such file or 
directory
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
    at java.lang.ProcessImpl.start(ProcessImpl.java:65)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)

On a normal linux machine (on which I am a sudoer) I can fix this by installing 
ia32lib libraries

on  the cluster it is a simple matter of doing the following:
#binary.blastall.2.2.6.path=bin/blast/2.2.6/blastall
binary.blastall.2.2.6.path=bin/blast/2.2.19/blastall

it seems to work and avoids using decade old code.

Should this cause any problems?  could the 2.2.6 blast be done away with?

Original issue reported on code.google.com by [email protected] on 22 May 2013 at 9:33

[interhelp #24415] Missing Gene3D matches

InterProScan version 5.5-48.0 cannot get matches for Gene3D from the 
precalculated match lookup service. As such, if you do not disable the use of 
the precalculated match lookup service.(using -dp or --disable-precalc) you 
will not get Gene3d matches.

Original issue reported on code.google.com by [email protected] on 30 Jul 2014 at 8:54

[interhelp #23153] multiple instances on same machine fail to finish

IPS fails to finish occasionally when running multiple instances on the same 
machine.

What steps will reproduce the problem?
1. Run 2 instances of IPS5 on the same machine

What is the expected output? What do you see instead?
Occasionally both IPS instances will run forever without doing anything.

Both instances still seem somehow busy (80% cpu usage for each of the java 
processes), but no worker threads seem to be spawned and no output tsv is being 
generated. 

Is it possible that IPS is doing some colliding file-locking?  To me the 
problem seems to occur early in the ips-workflow because no outputs are 
generated.


What version of the product are you using? On what operating system?
interproscan-5.4-47.0
cent-os with a lustre file-system

Please let me know if I should try anything else to narrow down the problem.

Original issue reported on code.google.com by [email protected] on 7 Jul 2014 at 9:48

[interhelp #15566] problems with running interproscan

What steps will reproduce the problem?
1../interproscan.sh

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

help menu... instead this:

28/02/2014 16:21:08:143 Welcome to InterProScan-5.3-46.0
Exception in thread "main" 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'htmlWriter' defined in class path resource 
[spring/jobs/outputWriter/html/htmlWriter-context.xml]: Cannot resolve 
reference to bean 'freeMarkerConfigHtmlWriter' while setting bean property 
'freeMarkerConfig'; nested exception is 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'freeMarkerConfigHtmlWriter' defined in class path resource 
[spring/jobs/outputWriter/html/htmlWriter-context.xml]: Initialization of bean 
failed; nested exception is org.springframework.beans.FatalBeanException: 
Failed to obtain BeanInfo for class [freemarker.template.Configuration]; nested 
exception is java.beans.IntrospectionException: type mismatch between read and 
write methods
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:328)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:106)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1360)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1118)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:609)
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918)
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:469)
        at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:139)
        at org.springframework.context.support.ClassPathXmlApplicationContext.<init>(ClassPathXmlApplicationContext.java:93)
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:128)
Caused by: org.springframework.beans.factory.BeanCreationException: Error 
creating bean with name 'freeMarkerConfigHtmlWriter' defined in class path 
resource [spring/jobs/outputWriter/html/htmlWriter-context.xml]: Initialization 
of bean failed; nested exception is 
org.springframework.beans.FatalBeanException: Failed to obtain BeanInfo for 
class [freemarker.template.Configuration]; nested exception is 
java.beans.IntrospectionException: type mismatch between read and write methods
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:527)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
        at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:322)
        ... 15 more
Caused by: org.springframework.beans.FatalBeanException: Failed to obtain 
BeanInfo for class [freemarker.template.Configuration]; nested exception is 
java.beans.IntrospectionException: type mismatch between read and write methods
        at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:262)
        at org.springframework.beans.CachedIntrospectionResults.forClass(CachedIntrospectionResults.java:149)
        at org.springframework.beans.BeanWrapperImpl.getCachedIntrospectionResults(BeanWrapperImpl.java:324)
        at org.springframework.beans.BeanWrapperImpl.getPropertyDescriptors(BeanWrapperImpl.java:331)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.filterPropertyDescriptorsForDependencyCheck(AbstractAutowireCapableBeanFactory.java:1242)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1101)
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
        ... 21 more
Caused by: java.beans.IntrospectionException: type mismatch between read and 
write methods
        at java.beans.PropertyDescriptor.findPropertyType(PropertyDescriptor.java:659)
        at java.beans.PropertyDescriptor.setReadMethod(PropertyDescriptor.java:256)
        at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:282)
        at org.springframework.beans.ExtendedBeanInfo.addOrUpdatePropertyDescriptor(ExtendedBeanInfo.java:180)
        at org.springframework.beans.ExtendedBeanInfo.<init>(ExtendedBeanInfo.java:100)
        at org.springframework.beans.CachedIntrospectionResults.<init>(CachedIntrospectionResults.java:224)
        ... 27 more

What version of the product are you using? On what operating system?

InterProScan-5.3-46.0
Linux pathos 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 
x86_64 x86_64 x86_64 GNU/Linux

java version "1.8.0"
Java(TM) SE Runtime Environment (build 1.8.0-b129)
Java HotSpot(TM) 64-Bit Server VM (build 25.0-b69, mixed mode)
This is perl 5, version 14, subversion 2 (v5.14.2) built for 
x86_64-linux-gnu-thread-multi

Please provide any additional information below.

I followed the installation instructions and I'm not able to run interproscan.

Original issue reported on code.google.com by [email protected] on 28 Feb 2014 at 3:32

RC6 - workers exceed their maximum runtime by far

(I posted this issue to the google group by mistake)

What steps will reproduce the problem?

I set up RC6 to run on an SGE cluster. Since our cluster requires the user to 
supply a maximum run time for the jobs (h_rt limit) i set the h_rt limit in the 
worker qsub definitions in the properties file. I chose to request an h_rt 
double of 4h, when the maximum woker lifetime property was set to 7200s. 
Running an analysis of the test proteins files worked fine. However, running 
large protein set fails. The reason seems to be that the workers run far longer 
than the maximum run time, and when they have been running for 4h, they are 
killed by SGE, as their h_rt runs out. The master then stalls in a busy loop 
(100% cpu) and the analysis will not finish.


What version of the product are you using? On what operating system?
I5RC6

Please provide any additional information below.

It would be good if the workers adhere to the set maximum run time, and exit 
gracefully when it runs out in order for the master to launch new workers to 
replace those who have spent all their run time. This would give the benefit 
that workers can be launched onto compute nodes where the i5 jobs can be used 
to backfill slots reserved for coming jobs. This will allow for more efficient 
use of the computational resources.

Original issue reported on code.google.com by [email protected] on 4 May 2013 at 6:54

[interhelp #25610] InterProScan 5.6-48.0 is using InterPro version 47.0 data only

Will be fixed in version 5.7-48.0.

Original issue reported on code.google.com by [email protected] on 15 Aug 2014 at 8:57

interproscan 5RC7

1. when i use this command "./interproscan.sh -i test_proteins.fasta -f tsv" , 
it can run normally, but when i run "./interproscan.sh -i test_proteins.fasta 
-dp -f tsv",it occur error just as follow.(my system is suse linux server 11, 
24 cpu, 20G memory),could you tell me why?



jobTIGRFAM-13.0, jobProDom-2006.1, jobPanther-7.2, jobSMART-6.2, 
jobPrositeProfiles-20.89, jobPrositePatterns-20.89, jobSuperFamily-1.75, 
jobPRINTS-42.0, jobGene3d-3.5.0, jobPIRSF-2.83, jobPfamA-27.0, 
jobHAMAP-201302.26, jobCoils-2.2]
10/09/2013 22:32:49:560 Running InterProScan v5 in STANDALONE mode...
2013-09-10 22:32:49,561 
[uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:27] WARN - 
inVmWorkers min:8 max: 8
10/09/2013 22:32:55:922 first transaction ... 
Pre-calculated match lookup service DISABLED.  Please wait for match 
calculations to complete...
10/09/2013 22:32:56:148 first transaction ... done
10/09/2013 22:32:56:148 InterProScan analyses continue ....
2013-09-10 22:33:02,040 
[org.springframework.jms.listener.AbstractMessageListenerContainer:617] ERROR - 
Application exception overridden by rollback exception
java.lang.OutOfMemoryError: unable to create new native thread
    at java.lang.Thread.start0(Native Method)
    at java.lang.Thread.start(Thread.java:640)
    at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:105)
    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:123)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:86)
    at sun.reflect.GeneratedMethodAccessor62.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)

Original issue reported on code.google.com by [email protected] on 10 Sep 2013 at 2:39

PRINTS binary output parser storing the wrong evalue

The parser is storing the evalue from table 2 ("second level" annotation).  
Actually need to store the evalue from table 1 ("first level") as there is a 
rounding difference between the two.

This error may / will affect post processing.

Alex can provide further details.

Original issue reported on code.google.com by [email protected] on 14 Jul 2010 at 3:24

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