Hi there!
I’m trying to run InterProScan on a fasta file and I constantly get this bug:
Fatal error: Exit code 231 ()
Picked up _JAVA_OPTIONS: -Duser.home=/data/jwd07/main/000/105/870/105870435/home
log4j:WARN No appenders could be found for logger (org.apache.activemq.broker.BrokerService).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
java.lang.IllegalArgumentException: You have submitted a protein sequence which contains an asterix (*). This may be from an ORF prediction program. '*' is not a valid IUPAC amino acid character and amino acid sequences which go through our pipeline should not contain it. Please strip out all asterix characters from your sequence and resubmit your search.
at uk.ac.ebi.interpro.scan.model.Protein.setSequence(Protein.java:346)
at uk.ac.ebi.interpro.scan.model.Protein.setSequenceAndMd5(Protein.java:227)
at uk.ac.ebi.interpro.scan.model.Protein.<init>(Protein.java:134)
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.addToMoleculeCollectionInDB(LoadFastaFileIntoDBImpl.java:314)
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:149)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy138.loadSequences(Unknown Source)
at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadIntoDBStep.execute(FastaFileLoadIntoDBStep.java:282)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
at java.base/java.lang.Thread.run(Thread.java:829)
java.lang.IllegalArgumentException: You have submitted a protein sequence which contains an asterix (*). This may be from an ORF prediction program. '*' is not a valid IUPAC amino acid character and amino acid sequences which go through our pipeline should not contain it. Please strip out all asterix characters from your sequence and resubmit your search.
at uk.ac.ebi.interpro.scan.model.Protein.setSequence(Protein.java:346)
at uk.ac.ebi.interpro.scan.model.Protein.setSequenceAndMd5(Protein.java:227)
at uk.ac.ebi.interpro.scan.model.Protein.<init>(Protein.java:134)
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.addToMoleculeCollectionInDB(LoadFastaFileIntoDBImpl.java:314)
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:149)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy138.loadSequences(Unknown Source)
at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadIntoDBStep.execute(FastaFileLoadIntoDBStep.java:282)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
at java.base/java.lang.Thread.run(Thread.java:829)
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:43)
at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:169)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:413)
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
When I first tried to run the tool I got fatal Fatal error: Exit code 1 (), so I just disabled the applications with restricted license. But then I get the error code I showed above.
I don’t understand what might be wrong. Does someone have a clue?
Thank you very much for your work! Kind regards,
Teresa
