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ebi-pf-team / interproscan

Genome-scale protein function classification
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ERROR - Command line failed with exit code: 139 #229

Closed erroranderroranderror closed 4 months ago

erroranderroranderror commented 3 years ago

Hi, i'm using interproscan for functional annotation of new yeast strain.

However, it works and stops repeatedly with an error "ERROR - Command line failed with exit code: 139".

Please help me to resolve this problem.

version: 5.52-86.0

Command: command_route/interproscan.sh -i

Log: 10/09/2021 14:04:56:617 Welcome to InterProScan-5.52-86.0 10/09/2021 14:04:56:620 Running InterProScan v5 in STANDALONE mode... on Linux 10/09/2021 14:05:01:583 RunID: node04_20210910_140501201_kb24 10/09/2021 14:05:08:993 Loading file input.fasta 10/09/2021 14:05:08:995 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-33.1,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] 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. 10/09/2021 15:17:15:264 25% completed 10/09/2021 16:17:15:369 30% completed 10/09/2021 17:17:15:454 31% completed 10/09/2021 18:17:15:563 42% completed 10/09/2021 19:17:15:644 54% completed 10/09/2021 20:17:15:749 54% completed 10/09/2021 21:17:15:835 54% completed 10/09/2021 22:17:15:874 54% completed 10/09/2021 23:17:15:965 54% completed 11/09/2021 00:17:16:078 54% completed 11/09/2021 01:17:16:140 54% completed 11/09/2021 02:17:16:204 54% completed 11/09/2021 03:17:16:259 54% completed 11/09/2021 04:17:16:286 54% completed 11/09/2021 05:17:16:295 54% completed 11/09/2021 06:17:16:306 54% completed 11/09/2021 07:17:16:347 62% completed 11/09/2021 08:17:16:374 62% completed 11/09/2021 09:17:16:419 62% completed 11/09/2021 10:17:16:425 62% completed 11/09/2021 11:17:16:537 62% completed 11/09/2021 12:17:16:610 62% completed 11/09/2021 13:17:16:696 62% completed 11/09/2021 14:17:16:793 62% completed 2021-09-11 14:57:37,088 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 139 Command: bin/hmmer/hmmer3/3.3/hmmscan -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --cpu 1 -o myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.out --domtblout myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.domtblout.out data/panther/15.0/panther.hmm myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.fasta Error output from binary:

2021-09-11 14:57:37,438 [amqEmbeddedWorkerJmsContainer-4] [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: Command line failed with exit code: 139 Command: bin/hmmer/hmmer3/3.3/hmmscan -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --cpu 1 -o myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.out --domtblout myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.domtblout.out data/panther/15.0/panther.hmm myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.fasta Error output from binary:

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[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.GeneratedMethodAccessor97.invoke(Unknown Source) ~[?:?]
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:829) [?:?]

2021-09-11 14:57:37,699 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 139 Command: bin/hmmer/hmmer3/3.3/hmmscan -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --cpu 1 -o myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.out --domtblout myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.domtblout.out data/panther/15.0/panther.hmm myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.fasta Error output from binary:

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
at jdk.internal.reflect.GeneratedMethodAccessor97.invoke(Unknown Source)
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)

2021-09-11 14:57:37,711 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPantherRunHmmer3 2021-09-11 14:57:37,941 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:176] WARN - StepInstance 53 is being re-run following a failure. 11/09/2021 15:17:16:834 62% completed 11/09/2021 16:17:16:923 66% completed 11/09/2021 17:17:16:951 66% completed 11/09/2021 18:17:16:972 66% completed 11/09/2021 19:17:17:062 66% completed 11/09/2021 20:17:17:073 73% completed 11/09/2021 21:17:17:074 73% completed 11/09/2021 22:17:17:148 73% completed 11/09/2021 23:17:17:257 73% completed 12/09/2021 00:17:17:268 73% completed 12/09/2021 01:17:17:369 73% completed 12/09/2021 02:17:17:379 73% completed 12/09/2021 03:17:17:453 73% completed 12/09/2021 04:17:17:493 73% completed 12/09/2021 05:17:17:569 73% completed 12/09/2021 06:17:17:677 73% completed 12/09/2021 07:17:17:745 73% completed 12/09/2021 08:17:17:779 73% completed 12/09/2021 09:17:17:876 73% completed 12/09/2021 10:17:17:898 73% completed 12/09/2021 11:17:18:000 73% completed 12/09/2021 12:17:18:110 73% completed 12/09/2021 13:17:18:138 73% completed 12/09/2021 14:17:18:245 73% completed 12/09/2021 15:17:18:259 73% completed 12/09/2021 16:17:18:362 73% completed 12/09/2021 17:17:18:394 73% completed 12/09/2021 18:17:18:492 73% completed 12/09/2021 19:17:18:562 77% completed 12/09/2021 20:17:18:603 77% completed 12/09/2021 21:17:18:693 77% completed 12/09/2021 22:17:18:779 77% completed 12/09/2021 23:17:18:823 77% completed 13/09/2021 00:17:18:908 77% completed 13/09/2021 01:17:18:942 77% completed 13/09/2021 02:17:18:972 77% completed 13/09/2021 03:17:19:086 77% completed 13/09/2021 04:17:19:136 77% completed 13/09/2021 05:17:19:217 77% completed 13/09/2021 06:17:19:233 77% completed 13/09/2021 07:17:19:268 77% completed 13/09/2021 08:17:19:334 77% completed 13/09/2021 09:17:19:375 77% completed 13/09/2021 10:17:19:390 77% completed 13/09/2021 11:17:19:447 77% completed 13/09/2021 12:17:19:534 77% completed 13/09/2021 13:17:19:574 77% completed 13/09/2021 14:17:19:629 77% completed 13/09/2021 15:17:19:631 77% completed 13/09/2021 16:17:19:705 77% completed 2021-09-13 16:19:16,072 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 139 Command: bin/hmmer/hmmer3/3.3/hmmscan -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --cpu 1 -o myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.out --domtblout myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.domtblout.out data/panther/15.0/panther.hmm myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.fasta Error output from binary:

2021-09-13 16:19:16,076 [amqEmbeddedWorkerJmsContainer-4] [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: Command line failed with exit code: 139 Command: bin/hmmer/hmmer3/3.3/hmmscan -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --cpu 1 -o myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.out --domtblout myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.domtblout.out data/panther/15.0/panther.hmm myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.fasta Error output from binary:

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[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.GeneratedMethodAccessor97.invoke(Unknown Source) ~[?:?]
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:829) [?:?]

2021-09-13 16:19:16,110 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 139 Command: bin/hmmer/hmmer3/3.3/hmmscan -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --cpu 1 -o myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.out --domtblout myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.domtblout.out data/panther/15.0/panther.hmm myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.fasta Error output from binary:

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
at jdk.internal.reflect.GeneratedMethodAccessor97.invoke(Unknown Source)
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)

2021-09-13 16:19:16,110 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPantherRunHmmer3 2021-09-13 16:19:16,165 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:176] WARN - StepInstance 53 is being re-run following a failure. 13/09/2021 17:17:19:816 80% completed 13/09/2021 18:17:19:895 80% completed 13/09/2021 19:17:19:921 80% completed 13/09/2021 20:17:19:962 80% completed 13/09/2021 21:17:20:020 80% completed 13/09/2021 22:17:20:112 80% completed 13/09/2021 23:17:20:139 80% completed 14/09/2021 00:17:20:171 80% completed 14/09/2021 01:17:20:255 80% completed 14/09/2021 02:17:20:297 80% completed 14/09/2021 03:17:20:380 80% completed 14/09/2021 04:17:20:452 80% completed 14/09/2021 05:17:20:568 80% completed 14/09/2021 06:17:20:660 80% completed 14/09/2021 07:17:20:668 80% completed 14/09/2021 08:17:20:739 80% completed 14/09/2021 09:17:20:787 80% completed 14/09/2021 10:17:20:792 80% completed 14/09/2021 11:17:20:815 80% completed 14/09/2021 12:17:20:902 80% completed 14/09/2021 13:17:20:907 80% completed 2021-09-14 13:42:26,133 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 139 Command: bin/hmmer/hmmer3/3.3/hmmscan -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --cpu 1 -o myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.out --domtblout myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.domtblout.out data/panther/15.0/panther.hmm myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.fasta Error output from binary:

2021-09-14 13:42:26,146 [amqEmbeddedWorkerJmsContainer-7] [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: Command line failed with exit code: 139 Command: bin/hmmer/hmmer3/3.3/hmmscan -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --cpu 1 -o myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.out --domtblout myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.domtblout.out data/panther/15.0/panther.hmm myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.fasta Error output from binary:

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[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.GeneratedMethodAccessor97.invoke(Unknown Source) ~[?:?]
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:829) [?:?]

2021-09-14 13:42:26,201 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : java.lang.IllegalStateException: Command line failed with exit code: 139 Command: bin/hmmer/hmmer3/3.3/hmmscan -Z 65000000 -E 0.001 --domE 0.00000001 --incdomE 0.00000001 --cpu 1 -o myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.out --domtblout myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.raw.domtblout.out data/panther/15.0/panther.hmm myroute/temp/server_20210910_140501201_kb24//jobPanther/000000000001_000000000007.fasta Error output from binary:

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
at jdk.internal.reflect.GeneratedMethodAccessor97.invoke(Unknown Source)
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)

2021-09-14 13:42:26,201 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPantherRunHmmer3 2021-09-14 13:42:26,265 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 53 : Run HMMER 3 Binary for selected proteins for proteins 1 to 7 has failed irretrievably. Available StackTraces follow. 2021-09-14 13:42:26,265 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status. 2021-09-14 13:42:26,270 [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

Thank you.

matthiasblum commented 3 years ago

Hi,

What is printed when running ./interproscan.sh?

Thank you

erroranderroranderror commented 3 years ago

Hi, matthiasblum.

When i run ./interproscan.sh, following descriptions are appeared:

16/09/2021 14:02:39:646 Welcome to InterProScan-5.52-86.0 16/09/2021 14:02:39:650 Running InterProScan v5 in STANDALONE mode... on Linux usage: java -XX:+UseParallelGC -XX:ParallelGCThreads=2 -XX:+AggressiveOpts -XX:+UseFastAccessorMethods -Xms128M -Xmx2048M -jar interproscan-5.jar

Please give us your feedback by sending an email to

interhelp@ebi.ac.uk

-appl,--applications Optional, comma separated list of analyses. If this option is not set, ALL analyses will be run. -b,--output-file-base Optional, base output filename (relative or absolute path). Note that this option, the --output-dir (-d) option and the --outfile (-o) option are mutually exclusive. The appropriate file extension for the output format(s) will be appended automatically. By default the input file path/name will be used. -cpu,--cpu Optional, number of cores for inteproscan. -d,--output-dir Optional, output directory. Note that this option, the --outfile (-o) option and the --output-file-base (-b) option are mutually exclusive. The output filename(s) are the same as the input filename, with the appropriate file extension(s) for the output format(s) appended automatically . -dp,--disable-precalc Optional. Disables use of the precalculated match lookup service. All match calculations will be run locally. -dra,--disable-residue-annot Optional, excludes sites from the XML, JSON output -etra,--enable-tsv-residue-annot Optional, includes sites in TSV output -exclappl,--excl-applications Optional, comma separated list of analyses you want to exclude. -f,--formats Optional, case-insensitive, comma separated list of output formats. Supported formats are TSV, XML, JSON, GFF3, HTML and SVG. Default for protein sequences are TSV, XML and GFF3, or for nucleotide sequences GFF3 and XML. -goterms,--goterms Optional, switch on lookup of corresponding Gene Ontology annotation (IMPLIES -iprlookup option) -help,--help Optional, display help information -i,--input Optional, path to fasta file that should be loaded on Master startup. Alternatively, in CONVERT mode, the InterProScan 5 XML file to convert. -incldepappl,--incl-dep-applications Optional, comma separated list of deprecated analyses that you want included. If this option is not set, deprecated analyses will not run. -iprlookup,--iprlookup Also include lookup of corresponding InterPro annotation in the TSV and GFF3 output formats. -ms,--minsize Optional, minimum nucleotide size of ORF to report. Will only be considered if n is specified as a sequence type. Please be aware of the fact that if you specify a too short value it might be that the analysis takes a very long time! -o,--outfile Optional explicit output file name (relative or absolute path). Note that this option, the --output-dir (-d) option and the --output-file-base (-b) option are mutually exclusive. If this option is given, you MUST specify a single output format using the -f option. The output file name will not be modified. Note that specifying an output file name using this option OVERWRITES ANY EXISTING FILE. -pa,--pathways Optional, switch on lookup of corresponding Pathway annotation (IMPLIES -iprlookup option) -t,--seqtype Optional, the type of the input sequences (dna/rna (n) or protein (p)). The default sequence type is protein. -T,--tempdir Optional, specify temporary file directory (relative or absolute path). The default location is temp/. -verbose,--verbose Optional, display more verbose log output -version,--version Optional, display version number -vl,--verbose-level Optional, display verbose log output at level specified. -vtsv,--output-tsv-version Optional, includes a TSV version file along with any TSV output (when TSV output requested) Copyright © EMBL European Bioinformatics Institute, Hinxton, Cambridge, UK. (http://www.ebi.ac.uk) The InterProScan software itself is provided under the Apache License, Version 2.0 (http://www.apache.org/licenses/LICENSE-2.0.html). Third party components (e.g. member database binaries and models) are subject to separate licensing - please see the individual member database websites for details.

Available analyses: TIGRFAM (15.0) : TIGRFAMs are protein families based on hidden Markov models (HMMs). SFLD (4) : SFLD is a database of protein families based on hidden Markov models (HMMs). SUPERFAMILY (1.75) : SUPERFAMILY is a database of structural and functional annotations for all proteins and genomes. PANTHER (15.0) : The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Gene3D (4.3.0) : Structural assignment for whole genes and genomes using the CATH domain structure database. Hamap (2020_05) : High-quality Automated and Manual Annotation of Microbial Proteomes. Coils (2.2.1) : Prediction of coiled coil regions in proteins. ProSiteProfiles (2021_01) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. SMART (7.1) : SMART allows the identification and analysis of domain architectures based on hidden Markov models (HMMs). CDD (3.18) : CDD predicts protein domains and families based on a collection of well-annotated multiple sequence alignment models. PRINTS (42.0) : A compendium of protein fingerprints - a fingerprint is a group of conserved motifs used to characterise a protein family. PIRSR (2021_02) : PIRSR is a database of protein families based on hidden Markov models (HMMs) and Site Rules. ProSitePatterns (2021_01) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. Pfam (33.1) : A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). MobiDBLite (2.0) : Prediction of intrinsically disordered regions in proteins. PIRSF (3.10) : The PIRSF concept is used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.

Deactivated analyses: SignalP_EUK (4.1) : Analysis SignalP_EUK is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp SignalP_GRAM_POSITIVE (4.1) : Analysis SignalP_GRAM_POSITIVE is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp SignalP_GRAM_NEGATIVE (4.1) : Analysis SignalP_GRAM_NEGATIVE is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp TMHMM (2.0c) : Analysis TMHMM is deactivated, because the resources expected at the following paths do not exist: bin/tmhmm/2.0c/decodeanhmm, data/tmhmm/2.0c/TMHMM2.0c.model Phobius (1.01) : Analysis Phobius is deactivated, because the resources expected at the following paths do not exist: bin/phobius/1.01/phobius.pl

Thank you.