ERROR:Is there something wrong with my JVM?

[yoyohashao]

Hello, I wanted to perform SUPERFAMILY prediction via interproscan but I got some error messages. It never happened before. Can you tell me what should I do? Many thanks. (I also attached some of my sequences) test.txt

08/09/2016 16:37:21:639 Welcome to InterProScan-5.19-58.0 08/09/2016 16:37:27:326 Running InterProScan v5 in STANDALONE mode... on Linux 08/09/2016 16:37:39:003 Loading file /Users/dragon/lipase-commercial-aa/ 08/09/2016 16:37:39:007 Running the following analyses: [SUPERFAMILY-1.75] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... 2016-09-08 16:37:39,021 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back. java.lang.IllegalStateException: Could not read the fastaFileInputStream. at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:136) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207) at com.sun.proxy.$Proxy93.loadSequences(Unknown Source) at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep.execute(FastaFileLoadStep.java:245) 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:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207) at com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source) at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189) at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746) at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684) at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.IOException: Is a directory at sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.FileDispatcherImpl.read(FileDispatcherImpl.java:46) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:197) at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:159) at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65) at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109) at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:62) ... 38 more 2016-09-08 16:37:39,025 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepLoadFromFasta 2016-09-08 16:37:39,112 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:76] WARN - StepInstance 1 is being re-run following a failure. 08/09/2016 16:37:39:127 Loading file /Users/dragon/lipase-commercial-aa/ 08/09/2016 16:37:39:128 Running the following analyses: [SUPERFAMILY-1.75] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... 2016-09-08 16:37:39,129 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:199] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back. java.lang.IllegalStateException: Could not read the fastaFileInputStream. at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:136) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207) at com.sun.proxy.$Proxy93.loadSequences(Unknown Source) at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadStep.execute(FastaFileLoadStep.java:245) 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:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207) at com.sun.proxy.$Proxy96.executeInTransaction(Unknown Source) at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:189) at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:746) at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:684) at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:651) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:315) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:253) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1150) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1142) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1039) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.IOException: Is a directory at sun.nio.ch.FileDispatcherImpl.read0(Native Method) at sun.nio.ch.FileDispatcherImpl.read(FileDispatcherImpl.java:46) at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223) at sun.nio.ch.IOUtil.read(IOUtil.java:197) at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:159) at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65) at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109) at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103) at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284) at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326) at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178) at java.io.InputStreamReader.read(InputStreamReader.java:184) at java.io.BufferedReader.fill(BufferedReader.java:161) at java.io.BufferedReader.readLine(BufferedReader.java:324) at java.io.BufferedReader.readLine(BufferedReader.java:389) at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileImpl.loadSequences(LoadFastaFileImpl.java:62) ... 38 more 2016-09-08 16:37:39,131 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:201] ERROR - StepExecution with errors - stepName: stepLoadFromFasta 2016-09-08 16:37:39,245 [main] [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. 2016-09-08 16:37:39,246 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:41] FATAL - The JVM will now exit with a non-zero exit status. 2016-09-08 16:37:39,246 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:149] 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:67) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:327) InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

[mifraser]

Hi,

What command are you using to run InterProScan? This error could happen because the "-i" input needs to be the filename of a FASTA sequence file, rather than a directory.

Thanks,

Matt

[yoyohashao]

Hey Matthew, the command line was: ./interproscan -i all-265aa.fa -appl SUPERFAMILY -f tsv I had used similar command lines before and I got the results I needed. But suddenly it doesn't work

On Sep 9, 2016 18:08, "Matthew Fraser" notifications@github.com wrote:

Hi,

What command are you using to run InterProScan? This error could happen because the "-i" input needs to be the filename of a FASTA sequence file, rather than a directory.

Thanks,

Matt

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ebi-pf-team/interproscan/issues/14#issuecomment-245873816, or mute the thread https://github.com/notifications/unsubscribe-auth/AHTXDyReL5QG1q1RHKbOwMajtQmi3weyks5qoTAVgaJpZM4J3xHD .

[mifraser]

Sorry for the late reply. Did you solve this?

You are using Java 8 I assume? It appears that InterProScan couldn't read the input file properly. Is "all-265aa.fa" a FASTA file?

The error mentions "IllegalStateException: Could not read the fastaFileInputStream" and "Caused by: java.io.IOException: Is a directory". The input needs to be a FASTA file and not a directory which should explain this. If not then it would need more investigation!

Kind regards,

Matt