unixprocess+java+186_interproscan 的使用和遇到的问题
运行interproscan时报错:
[Wed Oct 08 13:07:16]
cmiao@apple /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0
$ ./interproscan.sh -i test_proteins.fasta
08/10/2014 13:08:53:591 Welcome to InterProScan-5.7-48.0
08/10/2014 13:09:06:297 Running InterProScan v5 in STANDALONE mode...
Loading file /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/test_proteins.fasta
08/10/2014 13:09:21:009 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]
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.
08/10/2014 13:09:27:248 29% completed
2014-10-08 13:09:32,238 [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: IOException thrown when attempting to run binary
at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:130)
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:57)
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.$Proxy96.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:181)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
at org.springframework.jms.listener.DefaultMessageListenerContainer$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:745)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1047)
at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:144)
at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:128)
... 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.(UNIXProcess.java:186)
at java.lang.ProcessImpl.start(ProcessImpl.java:130)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1028)
... 24 more
2014-10-08 13:09:32,320 [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:56] WARN - StepInstance 3 is being re-run following a failure.
2014-10-08 13:09:37,341 [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: IOException thrown when attempting to run binary
at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:130)
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:57)
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.$Proxy96.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:181)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
at org.springframework.jms.listener.DefaultMessageListenerContainer$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:745)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1047)
at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:144)
at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:128)
... 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.(UNIXProcess.java:186)
at java.lang.ProcessImpl.start(ProcessImpl.java:130)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1028)
... 24 more
2014-10-08 13:09:37,399 [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:56] WARN - StepInstance 3 is being re-run following a failure.
2014-10-08 13:09:42,420 [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: IOException thrown when attempting to run binary
at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:130)
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:57)
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.$Proxy96.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:181)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:562)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:500)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:468)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:326)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:264)
at org.springframework.jms.listener.DefaultMessageListenerContainer$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:745)
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1047)
at uk.ac.ebi.interpro.scan.io.cli.CommandLineConversationImpl.runCommand(CommandLineConversationImpl.java:144)
at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:128)
... 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.(UNIXProcess.java:186)
at java.lang.ProcessImpl.start(ProcessImpl.java:130)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1028)
... 24 more
2014-10-08 13:09:42,510 [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:24] FATAL - Analysis step 3 : Run fingerprintscan Binary for selected proteins for proteins 1 to 5 has failed irretrievably. Available StackTraces follow.
2014-10-08 13:09:42,510 [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status.
2014-10-08 13:09:42,511 [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:270)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
本来以为是java的问题, 以为要把openJDK 换成JRE, 但是问了老师,没那回事,最关键的问题是这句:
Caused by: java.io.IOException: Cannot run program "bin/coils/ncoils": error=2, No such file or directory
说明ncoils没法运行。是ncoils的问题, google后发现:
所以要重新搞个ncoils把以前的给替换掉。
步骤:
mkdir tmp
cd tmp
tar zxvf ncoils.tar.gz
cd coils/
要把coils加到环境变量里:
export COILSDIR=/share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/tmp/coils
echo $COILSDIR
这样是暂时的,永久性的需要编辑你的./bash_profile 然后source ~/.bash_profile生效
cd /share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/bin/coils
将旧的移除新的加入
mv ncoils ncoils.bak
cp ../../tmp/coils/ncoils-osf ncoils
问题解决!
by freemao
FAFU
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