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ebi-pf-team / interproscan

Genome-scale protein function classification
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InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details #292

Open 1457634627 opened 2 years ago

1457634627 commented 2 years ago 
04/10/2022 19:46:59:463 Welcome to InterProScan-5.55-88.0
04/10/2022 19:46:59:463 Running InterProScan v5 in STANDALONE mode... on Linux
04/10/2022 19:47:13:167 RunID: iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98
04/10/2022 19:47:34:309 Loading file /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/test_proteins.fasta
04/10/2022 19:47:34:310 Running the following analyses:
[AntiFam-7.0,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_05,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.
2022-10-04 19:47:37,307 [Thread-6] [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:748] WARN - 

The version of InterProScan you are using is 5.55-88.0
The version of the lookup service you are using is 5.57-90.0
As the data in these versions is not the same, you cannot use this match lookup service.
InterProScan will now run locally
If you would like to use the match lookup service, you have the following options:
i) Download the newest version of InterProScan5 from our FTP site by following the instructions on:
   https://www.ebi.ac.uk/interpro/interproscan.html
ii) Download the match lookup service for your version of InterProScan from our FTP site and install it locally.
    You will then need to edit the following property in your configuration file to point to your local installation:
    precalculated.match.lookup.service.url=

In the meantime, the analysis will continue to run locally.

2022-10-04 19:47:45,118 [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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.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

2022-10-04 19:47:45,120 [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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.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-5.55-88.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:577) ~[?:?]
    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 jdk.proxy2.$Proxy144.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833) [?:?]
2022-10-04 19:47:45,140 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.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)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
    at java.base/java.lang.reflect.Method.invoke(Method.java:577)
    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 jdk.proxy2/jdk.proxy2.$Proxy144.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833)
2022-10-04 19:47:45,143 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepGene3dRunHmmer3
2022-10-04 19:47:45,178 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:176] WARN - StepInstance 54 is being re-run following a failure.
04/10/2022 19:47:51:749 26% completed
2022-10-04 19:47:56,327 [amqEmbeddedWorkerJmsContainer-2] [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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.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

2022-10-04 19:47:56,327 [amqEmbeddedWorkerJmsContainer-2] [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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.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-5.55-88.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:577) ~[?:?]
    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 jdk.proxy2.$Proxy144.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833) [?:?]
2022-10-04 19:47:56,329 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194712867_im98//jobGene3d/000000000001_000000000001.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)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
    at java.base/java.lang.reflect.Method.invoke(Method.java:577)
    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 jdk.proxy2/jdk.proxy2.$Proxy144.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833)
2022-10-04 19:47:56,331 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepGene3dRunHmmer3
2022-10-04 19:47:56,400 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:176] WARN - StepInstance 54 is being re-run following a failure.
^Z
[2]+  Stopped                 ./interproscan.sh -i test_proteins.fasta
[root@iZ8vb4s0jlsfk2x77wsvruZ interproscan-5.55-88.0]# ./interproscan.sh -i test_proteins.fasta 
04/10/2022 19:49:12:250 Welcome to InterProScan-5.55-88.0
04/10/2022 19:49:12:251 Running InterProScan v5 in STANDALONE mode... on Linux
04/10/2022 19:49:24:479 RunID: iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4
04/10/2022 19:49:44:220 Loading file /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/test_proteins.fasta
04/10/2022 19:49:44:230 Running the following analyses:
[AntiFam-7.0,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_05,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.
2022-10-04 19:49:47,616 [Thread-6] [uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup:748] WARN - 

The version of InterProScan you are using is 5.55-88.0
The version of the lookup service you are using is 5.57-90.0
As the data in these versions is not the same, you cannot use this match lookup service.
InterProScan will now run locally
If you would like to use the match lookup service, you have the following options:
i) Download the newest version of InterProScan5 from our FTP site by following the instructions on:
   https://www.ebi.ac.uk/interpro/interproscan.html
ii) Download the match lookup service for your version of InterProScan from our FTP site and install it locally.
    You will then need to edit the following property in your configuration file to point to your local installation:
    precalculated.match.lookup.service.url=

In the meantime, the analysis will continue to run locally.

2022-10-04 19:50:00,836 [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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.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

2022-10-04 19:50:00,837 [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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.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-5.55-88.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:577) ~[?:?]
    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 jdk.proxy2.$Proxy144.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833) [?:?]
2022-10-04 19:50:00,872 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.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)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
    at java.base/java.lang.reflect.Method.invoke(Method.java:577)
    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 jdk.proxy2/jdk.proxy2.$Proxy144.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833)
2022-10-04 19:50:00,883 [amqEmbeddedWorkerJmsContainer-5] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepGene3dRunHmmer3
2022-10-04 19:50:01,000 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:176] WARN - StepInstance 14 is being re-run following a failure.
04/10/2022 19:50:02:642 26% completed
2022-10-04 19:50:13,470 [amqEmbeddedWorkerJmsContainer-3] [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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.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

2022-10-04 19:50:13,470 [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: Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.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-5.55-88.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:577) ~[?:?]
    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 jdk.proxy2.$Proxy144.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833) [?:?]
2022-10-04 19:50:13,471 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.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)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
    at java.base/java.lang.reflect.Method.invoke(Method.java:577)
    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 jdk.proxy2/jdk.proxy2.$Proxy144.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833)
2022-10-04 19:50:13,476 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepGene3dRunHmmer3
2022-10-04 19:50:13,510 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:176] WARN - StepInstance 14 is being re-run following a failure.
04/10/2022 19:50:15:742 51% completed
2022-10-04 19:50:25,245 [amqEmbeddedWorkerJmsContainer-3] [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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.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

2022-10-04 19:50:25,245 [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: Command line failed with exit code: 1
Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.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-5.55-88.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) ~[?:?]
    at java.lang.reflect.Method.invoke(Method.java:577) ~[?:?]
    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 jdk.proxy2.$Proxy144.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.1.6.RELEASE.jar:5.1.6.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833) [?:?]
2022-10-04 19:50:25,250 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
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 /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.out --domtblout /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.raw.domtblout.out data/gene3d/4.3.0/gene3d_main.hmm /bio/yzj/tools/Interproscan/interproscan-5.55-88.0/temp/iZ8vb4s0jlsfk2x77wsvruZ_20221004_194924291_5xl4//jobGene3d/000000000001_000000000001.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)
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
    at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104)
    at java.base/java.lang.reflect.Method.invoke(Method.java:577)
    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 jdk.proxy2/jdk.proxy2.$Proxy144.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$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:833)
2022-10-04 19:50:25,251 [amqEmbeddedWorkerJmsContainer-3] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepGene3dRunHmmer3
2022-10-04 19:50:25,373 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 14 : Run HMMER3 for proteins 1 to 1 has failed irretrievably.  Available StackTraces follow.
2022-10-04 19:50:25,374 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
2022-10-04 19:50:25,374 [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)

There is no problem running the instance file. But with any other protein file, this is the problem. How does the centos system solve this problem？

NicMAlexandre commented 2 years ago

I am getting the same issue

tear-wy commented 1 year ago

I'm having the same problem, but it was working fine before

tgrego commented 1 year ago

It looks like an issue with the pressed models. try repressing the models by running on the installation directory: python3 setup.py --force interproscan.properties

yangruixue-xue commented 1 month ago

It looks like an issue with the pressed models. try repressing the models by running on the installation directory: python3 setup.py --force interproscan.properties

Sorry,this also can not,you have success?