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ebi-pf-team / interproscan

Genome-scale protein function classification
Apache License 2.0
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Interpro running error #263

Closed ap1438 closed 9 months ago

ap1438 commented 2 years ago

(interproscan) [group_01@mn01 Test]$ interproscan.sh -i Amino_Acid.fasta -f tsv -dp 20/04/2022 13:04:57:322 Welcome to InterProScan-5.54-87.0 20/04/2022 13:04:57:324 Running InterProScan v5 in STANDALONE mode... on Linux java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1167) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.iq80.leveldb.impl.DbLock.(DbLock.java:47) at org.iq80.leveldb.impl.DbImpl.(DbImpl.java:169) at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41) at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStores(Run.java:1710) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:471) java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1167) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.iq80.leveldb.impl.DbLock.(DbLock.java:47) at org.iq80.leveldb.impl.DbImpl.(DbImpl.java:169) at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41) at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStores(Run.java:1714) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:471) java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1167) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.iq80.leveldb.impl.DbLock.(DbLock.java:47) at org.iq80.leveldb.impl.DbImpl.(DbImpl.java:169) at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41) at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStores(Run.java:1722) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:471) java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1167) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.iq80.leveldb.impl.DbLock.(DbLock.java:47) at org.iq80.leveldb.impl.DbImpl.(DbImpl.java:169) at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41) at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStores(Run.java:1726) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:471) java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1167) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.iq80.leveldb.impl.DbLock.(DbLock.java:47) at org.iq80.leveldb.impl.DbImpl.(DbImpl.java:169) at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41) at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStoreEntry(Run.java:1764) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:472) 2022-04-20 13:05:12,321 [main] [uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl:244] WARN - proteinsNotInLookupDB is NULL - storename: proteinNotInLookupDB dbmane: proteinNotInLookupDB 20/04/2022 13:05:12:337 RunID: mn01.aryabhatta.local_20220420_130512081_eksk 20/04/2022 13:05:28:918 Loading file /home/internal/Sys_Bio/group_gaurav01/anaconda3/envs/interproscan/bin/Test/Amino_Acid.fasta 20/04/2022 13:05:28:922 Running the following analyses: [CDD-3.18,Coils-2.2.1,Gene3D-4.3.0,Hamap-2020_05,MobiDBLite-2.0,PANTHER-15.0,Pfam-34.0,PIRSF-3.10,PIRSR-2021_02,PRINTS-42.0,ProSitePatterns-2021_01,ProSiteProfiles-2021_01,SFLD-4,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... java.lang.NullPointerException at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:78) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64) at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insert(ProteinDAOImpl.java:129) 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:343) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy78.insert(Unknown Source) at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:256) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy139.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:343) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) at java.base/java.lang.Thread.run(Thread.java:834) 2022-04-20 13:05:50,411 [amqEmbeddedWorkerJmsContainer-5] [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.IllegalStateException: Problem inserting data into the DBStore java.lang.NullPointerException at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:91) ~[interproscan-persistence-5.54-87.0.jar:?] at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64) ~[interproscan-persistence-5.54-87.0.jar:?] at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insert(ProteinDAOImpl.java:129) ~[interproscan-persistence-5.54-87.0.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:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at com.sun.proxy.$Proxy78.insert(Unknown Source) ~[?:?] at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:256) ~[interproscan-business-5.54-87.0.jar:?] at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?] at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?] at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?] at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?] at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at com.sun.proxy.$Proxy139.loadSequences(Unknown Source) ~[?:?] at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadIntoDBStep.execute(FastaFileLoadIntoDBStep.java:282) ~[interproscan-management-5.54-87.0.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:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) ~[?:?] at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?] at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at java.lang.Thread.run(Thread.java:834) [?:?] 2022-04-20 13:05:50,436 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Problem inserting data into the DBStore java.lang.NullPointerException at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:91) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64) at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insert(ProteinDAOImpl.java:129) 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:343) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy78.insert(Unknown Source) at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:256) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy139.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:343) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) at java.base/java.lang.Thread.run(Thread.java:834) 2022-04-20 13:05:50,438 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepLoadFromFastaIntoDB 2022-04-20 13:05:50,577 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:176] WARN - StepInstance 1 is being re-run following a failure. 20/04/2022 13:05:50:601 Loading file /home/internal/Sys_Bio/group_gaurav01/anaconda3/envs/interproscan/bin/Test/Amino_Acid.fasta 20/04/2022 13:05:50:603 Running the following analyses: [CDD-3.18,Coils-2.2.1,Gene3D-4.3.0,Hamap-2020_05,MobiDBLite-2.0,PANTHER-15.0,Pfam-34.0,PIRSF-3.10,PIRSR-2021_02,PRINTS-42.0,ProSitePatterns-2021_01,ProSiteProfiles-2021_01,SFLD-4,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... java.lang.NullPointerException at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:78) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64) at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insert(ProteinDAOImpl.java:129) 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:343) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy78.insert(Unknown Source) at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:256) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy139.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:343) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) at java.base/java.lang.Thread.run(Thread.java:834) 2022-04-20 13:06:08,345 [amqEmbeddedWorkerJmsContainer-1] [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.IllegalStateException: Problem inserting data into the DBStore java.lang.NullPointerException at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:91) ~[interproscan-persistence-5.54-87.0.jar:?] at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64) ~[interproscan-persistence-5.54-87.0.jar:?] at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insert(ProteinDAOImpl.java:129) ~[interproscan-persistence-5.54-87.0.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:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at com.sun.proxy.$Proxy78.insert(Unknown Source) ~[?:?] at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:256) ~[interproscan-business-5.54-87.0.jar:?] at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?] at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?] at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?] at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?] at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at com.sun.proxy.$Proxy139.loadSequences(Unknown Source) ~[?:?] at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadIntoDBStep.execute(FastaFileLoadIntoDBStep.java:282) ~[interproscan-management-5.54-87.0.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:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) ~[?:?] at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?] at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at java.lang.Thread.run(Thread.java:834) [?:?] 2022-04-20 13:06:08,346 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Problem inserting data into the DBStore java.lang.NullPointerException at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:91) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64) at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insert(ProteinDAOImpl.java:129) 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:343) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy78.insert(Unknown Source) at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:256) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy139.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:343) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) at java.base/java.lang.Thread.run(Thread.java:834) 2022-04-20 13:06:08,351 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepLoadFromFastaIntoDB 2022-04-20 13:06:08,405 [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. 2022-04-20 13:06:08,406 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status. 2022-04-20 13:06:08,406 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:349] 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:167) [interproscan-5.jar:?] at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:495) [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:167) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:495) InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details (interproscan) [groupgaurav01@mn01 Test]$ java -version openjdk version "11.0.1" 2018-10-16 LTS OpenJDK Runtime Environment Zulu11.2+3 (build 11.0.1+13-LTS) OpenJDK 64-Bit Server VM Zulu11.2+3 (build 11.0.1+13-LTS, mixed mode) (interproscan) [group@mn01 Test]$

I got this big error . Can anyone help me to resolve thi issue

I have centOS 7 And i have gone through issue #106 and checked . I have elfutils-libs [@mn01 interproscan]$ sudo yum install elfutils-libs Loaded plugins: langpacks Package elfutils-libs-0.168-8.el7.x86_64 already installed and latest version Nothing to do

matthiasblum commented 2 years ago

Hi @ap1438 ,

It looks like the file system does not support file locking. Are you running InterProScan on a network file system?

huang-qinyi commented 1 year ago

Have you ever solved this problem？I have the same problem..

matthiasblum commented 1 year ago

Hi @huang-qinyi,

Can you post the full logs, as well as the version of Java/InterProScan you are running, please?

huang-qinyi commented 1 year ago

command: nohup /home/software/interproscan-5.52-86.0//interproscan.sh -i test_proteins.fasta -o test_proteins.out -iprlookup -goterms -seqtype p -f TSV > nohuptest_proteins.fasta.log &

java -version

openjdk version "11.0.13" 2021-10-19 OpenJDK Runtime Environment JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21) OpenJDK 64-Bit Server VM JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21, mixed mode)

07/06/2023 14:44:21:091 Welcome to InterProScan-5.52-86.0 07/06/2023 14:44:21:099 Running InterProScan v5 in STANDALONE mode... on Linux java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1161) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.iq80.leveldb.impl.DbLock.(DbLock.java:47) at org.iq80.leveldb.impl.DbImpl.(DbImpl.java:169) at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41) at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStores(Run.java:1710) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:471) java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1161) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.iq80.leveldb.impl.DbLock.(DbLock.java:47) at org.iq80.leveldb.impl.DbImpl.(DbImpl.java:169) at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41) at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStores(Run.java:1714) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:471) java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1161) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.iq80.leveldb.impl.DbLock.(DbLock.java:47) at org.iq80.leveldb.impl.DbImpl.(DbImpl.java:169) at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41) at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStores(Run.java:1722) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:471) java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1161) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.iq80.leveldb.impl.DbLock.(DbLock.java:47) at org.iq80.leveldb.impl.DbImpl.(DbImpl.java:169) at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41) at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStores(Run.java:1726) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:471) java.io.IOException: Function not implemented at java.base/sun.nio.ch.FileDispatcherImpl.lock0(Native Method) at java.base/sun.nio.ch.FileDispatcherImpl.lock(FileDispatcherImpl.java:96) at java.base/sun.nio.ch.FileChannelImpl.tryLock(FileChannelImpl.java:1161) at java.base/java.nio.channels.FileChannel.tryLock(FileChannel.java:1165) at org.iq80.leveldb.impl.DbLock.(DbLock.java:47) at org.iq80.leveldb.impl.DbImpl.(DbImpl.java:169) at org.iq80.leveldb.impl.Iq80DBFactory.open(Iq80DBFactory.java:83) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.setLevelDBStore(LevelDBStore.java:41) at uk.ac.ebi.interpro.scan.jms.main.Run.configureKVStoreEntry(Run.java:1764) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:472) 2023-06-07 14:44:28,504 [main] [uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl:244] WARN - proteinsNotInLookupDB is NULL - storename: proteinNotInLookupDB dbmane: proteinNotInLookupDB 07/06/2023 14:44:28:510 RunID: fat01_20230607_144428150_3oxd 07/06/2023 14:44:39:762 Loading file /home/software/interproscan-5.52-86.0/test_proteins_redundant.fasta 07/06/2023 14:44:39:764 Running the following analyses: [Pfam-33.1] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... java.lang.NullPointerException at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:78) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64) at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insert(ProteinDAOImpl.java:129) 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:343) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy78.insert(Unknown Source) at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:256) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy139.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:343) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) at java.base/java.lang.Thread.run(Thread.java:829) 2023-06-07 14:44:53,861 [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.IllegalStateException: Problem inserting data into the DBStore java.lang.NullPointerException at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:91) ~[interproscan-persistence-5.52-86.0.jar:?] at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64) ~[interproscan-persistence-5.52-86.0.jar:?] at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insert(ProteinDAOImpl.java:129) ~[interproscan-persistence-5.52-86.0.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:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEAS E] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at com.sun.proxy.$Proxy78.insert(Unknown Source) ~[?:?] at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:256) ~[interproscan-business-5.52-86.0.jar:?] at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?] at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?] at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?] at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?] at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at com.sun.proxy.$Proxy139.loadSequences(Unknown Source) ~[?:?] at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadIntoDBStep.execute(FastaFileLoadIntoDBStep.java:282) ~[interproscan-management-5.52-86.0.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:343) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) ~[spring-tx-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.1.6.RELEASE.jar:5.1.6.RELEASE] at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source) ~[?:?] at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?] at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5 at com.sun.proxy.$Proxy142.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-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE] at java.lang.Thread.run(Thread.java:829) [?:?] 2023-06-07 14:44:53,879 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Problem inserting data into the DBStore java.lang.NullPointerException at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:91) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64) at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insert(ProteinDAOImpl.java:129) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy78.insert(Unknown Source) at uk.ac.ebi.interpro.scan.business.sequence.fasta.LoadFastaFileIntoDBImpl.loadSequences(LoadFastaFileIntoDBImpl.java:256) 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:343) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) 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:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy139.loadSequences(Unknown Source) at uk.ac.ebi.interpro.scan.management.model.implementations.stepInstanceCreation.proteinLoad.FastaFileLoadIntoDBStep.execute(FastaFileLoadIntoDBStep.java:282) at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) at com.sun.proxy.$Proxy142.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$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179) at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076) at java.base/java.lang.Thread.run(Thread.java:829) 2023-06-07 14:44:53,881 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepLoadFromFastaIntoDB 2023-06-07 14:44:53,957 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:176] WARN - StepInstance 1 is being re-run following a failure. 07/06/2023 14:44:53:988 Loading file /home/software/interproscan-5.52-86.0/test_proteins_redundant.fasta 07/06/2023 14:44:53:990 Running the following analyses: [Pfam-33.1] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... java.lang.NullPointerException at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:78) at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64) at uk.ac.ebi.interpro.scan.persistence.ProteinDAOImpl.insert(ProteinDAOImpl.java:129) ...

    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
    at java.base/java.lang.Thread.run(Thread.java:829)

2023-06-07 14:45:08,031 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepLoadFromFastaIntoDB 2023-06-07 14:45:08,158 [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. 2023-06-07 14:45:08,158 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status. 2023-06-07 14:45:08,159 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:349] 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:167) [interproscan-5.jar:?] at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:495) [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:167) at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:495) InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

matthiasblum commented 1 year ago

Hi @huang-qinyi,

It looks like it's the same issue, and your system does not support file lock. Are you using a shared file system (such as Lustre)? If so, you may need to contact your system admins to address the issue, or request a file system that supports file lock.