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ebi-pf-team / interproscan

Genome-scale protein function classification
Apache License 2.0
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ERROR - StepExecution with errors - stepName: stepCathGene3dRunHmmer3 #303

Closed lkiko closed 6 months ago

lkiko commented 1 year ago

Hello, I encountered the following problems when using this software. Do you have any suggestions for this problem?

`20/01/2023 12:45:30:407 Welcome to InterProScan-5.60-92.0 20/01/2023 12:45:30:410 Running InterProScan v5 in STANDALONE mode... on Linux 20/01/2023 12:45:37:263 RunID: zhangxclab001_20230120_124536448_h0cx 20/01/2023 12:45:51:745 Loading file /home/lanmeifang/interPro/interproscan-5.60-92.0/test/new-smo.pep 20/01/2023 12:45:51:746 Running the following analyses: [AntiFam-7.0,CDD-3.20,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2021_04,MobiDBLite-2.0,PANTHER-17.0,Pfam-35.0,PIRSF-3.10,PIRSR-2021_05,PRINTS-42.0,ProSitePatterns-2022_01,ProSiteProfiles-2022_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. 2023-01-20 12:46:13,270 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.out --domtblout /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.fasta Error output from binary:

Error: File format problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. Opened data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

2023-01-20 12:46:13,282 [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: 1 Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.out --domtblout /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.fasta Error output from binary:

Error: File format problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. Opened data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.60-92.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:568) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at jdk.proxy2.$Proxy142.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:833) [?:?]

2023-01-20 12:46:13,290 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2023-01-20 12:46:13,292 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepCathGene3dRunHmmer3 2023-01-20 12:46:13,423 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 23 is being re-run following a failure. 20/01/2023 12:46:13:571 25% completed 2023-01-20 12:46:21,135 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.out --domtblout /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.fasta Error output from binary:

Error: File format problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. Opened data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

2023-01-20 12:46:21,136 [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: 1 Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.out --domtblout /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.fasta Error output from binary:

Error: File format problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. Opened data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.60-92.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:568) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at jdk.proxy2.$Proxy142.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:833) [?:?]

2023-01-20 12:46:21,137 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2023-01-20 12:46:21,137 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepCathGene3dRunHmmer3 2023-01-20 12:46:21,235 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 23 is being re-run following a failure. 2023-01-20 12:46:21,553 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobFunFam/000000000001_000000000020.raw.out data/gene3d/4.3.0/gene3d_main.hmm /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobFunFam/000000000001_000000000020.fasta Error output from binary:

Error: File format problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. Opened data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

2023-01-20 12:46:21,554 [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: Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobFunFam/000000000001_000000000020.raw.out data/gene3d/4.3.0/gene3d_main.hmm /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobFunFam/000000000001_000000000020.fasta Error output from binary:

Error: File format problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. Opened data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.60-92.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:568) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at jdk.proxy2.$Proxy142.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:833) [?:?]

2023-01-20 12:46:21,555 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2023-01-20 12:46:21,556 [amqEmbeddedWorkerJmsContainer-1] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepCathFunFamRunHmmer3 2023-01-20 12:46:21,598 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 7 is being re-run following a failure. 2023-01-20 12:46:26,617 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.out --domtblout /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.fasta Error output from binary:

Error: File format problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. Opened data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

2023-01-20 12:46:26,618 [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: Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.out --domtblout /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /home/lanmeifang/interPro/interproscan-5.60-92.0/test/temp/zhangxclab001_20230120_124536448_h0cx//jobGene3d/000000000001_000000000020.fasta Error output from binary:

Error: File format problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. Opened data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.60-92.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:568) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at jdk.proxy2.$Proxy142.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.22.RELEASE.jar:5.2.22.RELEASE]
at java.lang.Thread.run(Thread.java:833) [?:?]

2023-01-20 12:46:26,619 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is : 2023-01-20 12:46:26,620 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepCathGene3dRunHmmer3 2023-01-20 12:46:26,656 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 23 : Run HMMER3 for proteins 1 to 20 has failed irretrievably. Available StackTraces follow. 2023-01-20 12:46:26,657 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status. 2023-01-20 12:46:26,657 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:363] ERROR - Exception thrown by StandaloneBlackBoxMaster: java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information. at uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError.failed(NonZeroExitOnUnrecoverableError.java:43) ~[interproscan-5.jar:?] at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:169) [interproscan-5.jar:?] at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:413) [interproscan-5.jar:?] ` And there is no log file in path ./temp/

matthiasblum commented 1 year ago

It looks like the SSI index for CATH-Gene3d are corrupted.

Try running the following command:

python3 setup.py --force interproscan.properties