interproscan 的使用和遇到的问题

时间：2014-10-09 02:06:07 阅读：1973 评论：0 收藏：0 [点我收藏+]

标签：http io os 使用 ar java for sp 2014

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.<init>(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.