InterProScan issue (FATAL ERROR)
Closed this issue · 1 comments
ValeroGracia commented
Hi there,
I am writing because after following the instructions in here for downloading the program in our cluster: (https://interproscan-docs.readthedocs.io/en/latest/HowToDownload.html);
and running the InterProScan test run reported here: (https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html) successfully,
I got the error messages below while using the command:
/home/albertva/Invertomics/Scripts/my_interproscan/interproscan-5.67-99.0/interproscan.sh -i /home/albertva/Invertomics/Nemertea_genomes/N59_Structural_Annotation/braker.aa -d /home/albertva/Invertomics/Nemertea_genomes/N59_Functional_Annotation -goterms -pa -verbose
Could you please help me to solve it?
Thank you very much in advance.
Best regards,
AVG
$ /home/albertva/Invertomics/Scripts/my_interproscan/interproscan-5.67-99.0/interproscan.sh -i /home/albertva/Invertomics/Nemertea_genomes/N59_Structural_Annotation/braker.aa -d /home/albertva/Invertomics/Nemertea_genomes/N59_Functional_Annotation -goterms -pa -verbose
23/04/2024 16:42:48:024 Welcome to InterProScan-5.67-99.0
23/04/2024 16:42:48:024 Running InterProScan v5 in STANDALONE mode... on Linux
23/04/2024 16:42:52:257 RunID: nhm01.hpc.uio.no_20240423_164252140_4533
23/04/2024 16:43:01:402 thread#: 64 Processing LoadFromFastaIntoDB JobNo #: 1 - stepInstanceId = 1 [000-000]
23/04/2024 16:43:01:404 Loading file /home/albertva/Invertomics/Nemertea_genomes/N59_Structural_Annotation/braker.aa
23/04/2024 16:43:01:406 Running the following analyses:
[AntiFam-7.0,CDD-3.20,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2023_05,MobiDBLite-2.0,NCBIfam-14.0,PANTHER-18.0,Pfam-36.0,PIRSF-3.10,PIRSR-2023_05,PRINTS-42.0,ProSitePatterns-2023_05,ProSiteProfiles-2023_05,SFLD-4,SMART-9.0,SUPERFAMILY-1.75]
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.
2024-04-23 16:43:01,418 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:216] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
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) ~[interproscan-model-5.67-99.0.jar:?]
at uk.ac.ebi.interpro.scan.model.Protein.setSequenceAndMd5(Protein.java:227) ~[interproscan-model-5.67-99.0.jar:?]
at uk.ac.ebi.interpro.scan.model.Protein.<init>(Protein.java:134) ~[interproscan-model-5.67-99.0.jar:?]
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.addToMoleculeCollectionInDB(LoadFastaFileIntoDBImpl.java:314) ~[interproscan-business-5.67-99.0.jar:?]
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:149) ~[interproscan-business-5.67-99.0.jar:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy138.loadSequences(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadIntoDBStep.execute(FastaFileLoadIntoDBStep.java:282) ~[interproscan-management-5.67-99.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at java.lang.Thread.run(Thread.java:834) [?:?]
2024-04-23 16:43:01,429 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
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:834)
2024-04-23 16:43:01,430 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepLoadFromFastaIntoDB
2024-04-23 16:43:01,505 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 1 is being re-run following a failure.
23/04/2024 16:43:01:512 thread#: 61 Processing LoadFromFastaIntoDB JobNo #: 2 - stepInstanceId = 1 [000-000]
23/04/2024 16:43:01:513 Loading file /home/albertva/Invertomics/Nemertea_genomes/N59_Structural_Annotation/braker.aa
23/04/2024 16:43:01:513 Running the following analyses:
[AntiFam-7.0,CDD-3.20,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2023_05,MobiDBLite-2.0,NCBIfam-14.0,PANTHER-18.0,Pfam-36.0,PIRSF-3.10,PIRSR-2023_05,PRINTS-42.0,ProSitePatterns-2023_05,ProSiteProfiles-2023_05,SFLD-4,SMART-9.0,SUPERFAMILY-1.75]
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.
2024-04-23 16:43:01,515 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:216] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
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) ~[interproscan-model-5.67-99.0.jar:?]
at uk.ac.ebi.interpro.scan.model.Protein.setSequenceAndMd5(Protein.java:227) ~[interproscan-model-5.67-99.0.jar:?]
at uk.ac.ebi.interpro.scan.model.Protein.<init>(Protein.java:134) ~[interproscan-model-5.67-99.0.jar:?]
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.addToMoleculeCollectionInDB(LoadFastaFileIntoDBImpl.java:314) ~[interproscan-business-5.67-99.0.jar:?]
at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:149) ~[interproscan-business-5.67-99.0.jar:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy138.loadSequences(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadIntoDBStep.execute(FastaFileLoadIntoDBStep.java:282) ~[interproscan-management-5.67-99.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at java.lang.Thread.run(Thread.java:834) [?:?]
2024-04-23 16:43:01,515 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
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:834)
2024-04-23 16:43:01,516 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepLoadFromFastaIntoDB
2024-04-23 16:43:01,620 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 1 : Load proteins from a fasta file and load into DB before creating required JobInstance objects for proteins null to null has failed irretrievably. Available StackTraces follow.
2024-04-23 16:43:01,621 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
2024-04-23 16:43:01,621 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:363] 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:43) ~[interproscan-5.jar:?]
at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:169) [interproscan-5.jar:?]
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:413) [interproscan-5.jar:?]
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)
23/04/2024 16:43:01:621 Exit status: 999
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details
matthiasblum commented
Hi @ValeroGracia, and sorry for the late reply.
Your input file seems to include a wildcard character (*), which is not a valid amino acid symbol.