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[interhelp #21071] failure likely related to blastall #39

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
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 macma...@gmail.com on 1 Jun 2014 at 1:12

GoogleCodeExporter commented 9 years ago 
Hi,

The binaries that we distribute with InterProScan should work on most linux 
systems. However, in some cases they may not work on a particular system. So 
the first thing to try is to get/compile your own version of the binary and 
update the relevant interproscan.properties to point at the new location.

Instructions on how to recompile blastall on your own system are given here:
https://code.google.com/p/interproscan/wiki/CompilingBinaries

Note that we use 2 different versions of blastall, but it looks like version 
2.2.6 was giving you your error.

https://code.google.com/p/interproscan/wiki/FAQ#7.Why_does_InterProScan_5_use_bl
astall_2.2.6_and_2.2.19?

If this doesn't solve the problem then just let us know!

Thanks,

Matthew

Original comment by Mr.Matth...@gmail.com on 2 Jun 2014 at 2:20

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 16 Jul 2014 at 1:49

GoogleCodeExporter commented 9 years ago 
Hi there, has this problem been solved? I have encountered exactly the same 
problem using the same version of InterProScan, InterProScan-5.4-47.0.

As for the 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

By simply replace blastall-2.2.6 with blastall-2.2.19, it completes 
successfully. Is there another way around the problem other than recompiling 
blastall from source, please?

Thanks,
Zhuyi

Original comment by alfred53...@gmail.com on 1 Oct 2014 at 11:09

GoogleCodeExporter commented 9 years ago 
Hi Zhuyi,

Thank you for the message! Although the compiled binaries we distribute should 
work on most Linux systems, they won't necessarily work on all.

I can confirm that the wiki documentation is all up-to-date in this area, FAQ 
items #3 and #7 still contain the latest advice on what you can try to get 
blastall 2.2.6 working. So other than recompiling, I don't know if you saw 
here...

https://code.google.com/p/interproscan/wiki/FAQ#3.What_should_I_do_if_one_of_the
_binaries_included_with_InterProScan_5_doesn%27t_work_on_my_system?

Hope that helps you get blastall 2.2.6 working!

Regards,

Matt
InterPro team

Original comment by Mr.Matth...@gmail.com on 2 Oct 2014 at 2:03

GoogleCodeExporter commented 9 years ago 
Hi Matt,

Thank you for your quick reply. I would like to add another bit of information. 
The sequence I have used to get the error is FLT3, which is of length 993. But 
if it is truncated into half, the error will be gone, which makes it seem to be 
related to the length of the sequence. It's wired, but that's what I have 
found. Similarly, for another two sequences I have tested, which are of lengths 
of 326 and 239, respectively. InterProScan also works. Do you have any comment 
on how this could be the case?

Regards,
Zhuyi

Original comment by alfred53...@gmail.com on 2 Oct 2014 at 3:21

GoogleCodeExporter commented 9 years ago 
Hi Matt,

I wonder where the blastall-2.2.19 that comes with InterProScan is from?

I downloaded 2.2.19 from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/, 
and surprisingly, the same problem persists, but it does not with the 
blastall-2.2.19 that came from InterProScan.

Regards,
Zhuyi

Original comment by alfred53...@gmail.com on 2 Oct 2014 at 4:45

GoogleCodeExporter commented 9 years ago 
Hi Matt,

I tried to avoid compiling from source as much as possible since debugging 
compilation errors is very time consuming, especially for the ncbi tool kit 
with blastall-2.2.6, which was released in 2003 and old.

After some experimentation, I have collected more information about the problem.

On Machine 1 with uname -a of 
Linux <HOSTNAME> 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Jan 3 21:39:27 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux

blast-2.2.19-ia32-linux.tar.gz doesn't work
blast-2.2.19-x64-linux.tar.gz  works
blast-2.2.6-ia32-linux.tar.gz  doesn't work
There is no blast-2.2.6-x64-linux compiled on 
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.6/

For Machine 2 with uname -a of
Linux <HOSTNAME> 2.6.18-371.1.2.el5 #1 SMP Tue Oct 22 12:51:53 EDT 2013 x86_64 
GNU/Linux
the blast-2.2.6 that comes with InterProScan just works.

Seemly, the error has something to do with the CPU architectures, but I don't 
have the knowledge to explain why this is the case. If you know why, please let 
me know. To me, the two machines don't have much difference since they're both 
of x86_64, but the same blastall works on one but not the other.

Regards,
Zhuyi

Original comment by alfred53...@gmail.com on 2 Oct 2014 at 5:08

GoogleCodeExporter commented 9 years ago 
Hi Zhuyi,

As you saw there is no blast-2.2.6-x64-linux compiled on the FTP site, that is 
why the 64-bit InterProScan 5 distribution contains a 32 bit binary as it is 
all we have available. As the InterProScan wiki mentions, one option to enable 
32-bit binaries to run on 64-bit Ubuntu (if you have that) is...

sudo apt-get install ia32-libs-multiarch
...or...
sudo apt-get install ia32-libs

Not all binaries work on every linux distribution. Sorry, I can't really 
comment on the blastall source code, it's not something we look into changing 
or anything as that's a bit beyond the scope of InterProScan 5 - we tend to 
just use the standard binaries in the same way the member database analysis 
does, to ensure we get the same results.

You could use blastall-2.2.19 in place of 2.2.6. It may work fine, but there is 
a small chance it may slightly affect your PIRSF 2.84 and Panther 9.0 results. 
This test would be interesting to add to our todo list, but I can't comment 
further at this stage...

So generally recompiling from source on your own system is the recommended 
option, but the two options above should also work!

Thanks,

Matt

Original comment by Mr.Matth...@gmail.com on 6 Oct 2014 at 2:24