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Run into java.lang.OutOfMemoryError problem after upgraded to InterProScan-5.72-103.0 #392

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irislin886 opened this issue Dec 2, 2024 · 7 comments
Open

Run into java.lang.OutOfMemoryError problem after upgraded to InterProScan-5.72-103.0 #392

irislin886 opened this issue Dec 2, 2024 · 7 comments

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@irislin886
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Hi, I have been using the 5.71-102.0-64-bit version of interproscan on my fasta files and I did not have anyproblem running it. However, when I tried to use it again, it showed:
"The version of InterProScan you are using is 5.71-102.0
The version of the lookup service you are using is 5.72-103.0
As the data in these versions is not the same, you cannot use this match lookup service.
InterProScan will now run locally"

So I followed the instruction a get the newest version which is 5.72-103.0 and reran it. However, I got the error message like this:
02/12/2024 14:53:34:011 Welcome to InterProScan-5.72-103.0
02/12/2024 14:53:34:012 Running InterProScan v5 in STANDALONE mode... on Linux
02/12/2024 14:53:39:008 RunID: tc123_20241202_145338288_bz6a
02/12/2024 14:53:48:846 Loading file /globalscratch/iris_job/46_annotated_Ref_Drosophila/5_InterProScan_prep/update/ananassae_significant_genes.fasta
02/12/2024 14:53:48:848 Running the following analyses:
[AntiFam-7.0,CDD-3.20,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2023_05,MobiDBLite-4.0,NCBIfam-15.0,PANTHER-19.0,Pfam-37.1,PIRSF-3.10,PIRSR-2023_05,PRINTS-42.0,ProSitePatterns-2023_05,ProSiteProfiles-2023_05,SFLD-4,SMART-9.0,SUPERFAMILY-1.75]
Available matches will be retrieved from the pre-calculated match lookup service.

Matches for any sequences that are not represented in the lookup service will be calculated locally.
org.iq80.leveldb.impl.DbImpl$BackgroundProcessingException: java.lang.OutOfMemoryError: Java heap space
at org.iq80.leveldb.impl.DbImpl.checkBackgroundException(DbImpl.java:421)
at org.iq80.leveldb.impl.DbImpl.writeInternal(DbImpl.java:683)
at org.iq80.leveldb.impl.DbImpl.put(DbImpl.java:649)
at org.iq80.leveldb.impl.DbImpl.put(DbImpl.java:642)
at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:78)
at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64)
at uk.ac.ebi.interpro.scan.persistence.MatchDAOImpl.persist(MatchDAOImpl.java:49)
at jdk.internal.reflect.GeneratedMethodAccessor88.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:205)
at jdk.proxy2/jdk.proxy2.$Proxy80.persist(Unknown Source)
at uk.ac.ebi.interpro.scan.precalc.berkeley.conversion.toi5.LookupStoreToI5ModelDAOImpl.persistMatch(LookupStoreToI5ModelDAOImpl.java:441)
at uk.ac.ebi.interpro.scan.precalc.berkeley.conversion.toi5.LookupStoreToI5ModelDAOImpl.populateProteinMatches(LookupStoreToI5ModelDAOImpl.java:340)
at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at jdk.proxy2/jdk.proxy2.$Proxy104.populateProteinMatches(Unknown Source)
at uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup.getPrecalculated(BerkeleyPrecalculatedProteinLookup.java:488)
at uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup.run(BerkeleyPrecalculatedProteinLookup.java:158)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.OutOfMemoryError: Java heap space
java.lang.IllegalStateException: Problem inserting data into the DBStore org.iq80.leveldb.impl.DbImpl$BackgroundProcessingException: java.lang.OutOfMemoryError: Java heap space
at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:91)
at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64)
at uk.ac.ebi.interpro.scan.persistence.MatchDAOImpl.persist(MatchDAOImpl.java:49)
at jdk.internal.reflect.GeneratedMethodAccessor88.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:205)
at jdk.proxy2/jdk.proxy2.$Proxy80.persist(Unknown Source)
at uk.ac.ebi.interpro.scan.precalc.berkeley.conversion.toi5.LookupStoreToI5ModelDAOImpl.persistMatch(LookupStoreToI5ModelDAOImpl.java:441)
at uk.ac.ebi.interpro.scan.precalc.berkeley.conversion.toi5.LookupStoreToI5ModelDAOImpl.populateProteinMatches(LookupStoreToI5ModelDAOImpl.java:340)
at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at jdk.proxy2/jdk.proxy2.$Proxy104.populateProteinMatches(Unknown Source)
at uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup.getPrecalculated(BerkeleyPrecalculatedProteinLookup.java:488)
at uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup.run(BerkeleyPrecalculatedProteinLookup.java:158)
at java.base/java.lang.Thread.run(Thread.java:833)
org.iq80.leveldb.impl.DbImpl$BackgroundProcessingException: java.lang.OutOfMemoryError: Java heap space
at org.iq80.leveldb.impl.DbImpl.checkBackgroundException(DbImpl.java:421)
at org.iq80.leveldb.impl.DbImpl.writeInternal(DbImpl.java:683)
at org.iq80.leveldb.impl.DbImpl.put(DbImpl.java:649)
at org.iq80.leveldb.impl.DbImpl.put(DbImpl.java:642)
at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:78)
at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64)
at uk.ac.ebi.interpro.scan.persistence.MatchDAOImpl.persist(MatchDAOImpl.java:49)
at jdk.internal.reflect.GeneratedMethodAccessor88.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:205)
at jdk.proxy2/jdk.proxy2.$Proxy80.persist(Unknown Source)
at uk.ac.ebi.interpro.scan.precalc.berkeley.conversion.toi5.LookupStoreToI5ModelDAOImpl.persistMatch(LookupStoreToI5ModelDAOImpl.java:441)
at uk.ac.ebi.interpro.scan.precalc.berkeley.conversion.toi5.LookupStoreToI5ModelDAOImpl.populateProteinMatches(LookupStoreToI5ModelDAOImpl.java:364)
at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at jdk.proxy2/jdk.proxy2.$Proxy104.populateProteinMatches(Unknown Source)
at uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup.getPrecalculated(BerkeleyPrecalculatedProteinLookup.java:488)
at uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup.run(BerkeleyPrecalculatedProteinLookup.java:158)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.OutOfMemoryError: Java heap space
java.lang.IllegalStateException: Problem inserting data into the DBStore org.iq80.leveldb.impl.DbImpl$BackgroundProcessingException: java.lang.OutOfMemoryError: Java heap space
at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:91)
at uk.ac.ebi.interpro.scan.persistence.kvstore.LevelDBStore.put(LevelDBStore.java:64)
at uk.ac.ebi.interpro.scan.persistence.MatchDAOImpl.persist(MatchDAOImpl.java:49)
at jdk.internal.reflect.GeneratedMethodAccessor88.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:205)
at jdk.proxy2/jdk.proxy2.$Proxy80.persist(Unknown Source)
at uk.ac.ebi.interpro.scan.precalc.berkeley.conversion.toi5.LookupStoreToI5ModelDAOImpl.persistMatch(LookupStoreToI5ModelDAOImpl.java:441)
at uk.ac.ebi.interpro.scan.precalc.berkeley.conversion.toi5.LookupStoreToI5ModelDAOImpl.populateProteinMatches(LookupStoreToI5ModelDAOImpl.java:364)
at jdk.internal.reflect.GeneratedMethodAccessor91.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at jdk.proxy2/jdk.proxy2.$Proxy104.populateProteinMatches(Unknown Source)
at uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup.getPrecalculated(BerkeleyPrecalculatedProteinLookup.java:488)
at uk.ac.ebi.interpro.scan.business.sequence.BerkeleyPrecalculatedProteinLookup.run(BerkeleyPrecalculatedProteinLookup.java:158)
at java.base/java.lang.Thread.run(Thread.java:833)
org.iq80.leveldb.impl.DbImpl$BackgroundProcessingException: java.lang.OutOfMemoryError: Java heap space
at org.iq80.leveldb.impl.DbImpl.checkBackgroundException(DbImpl.java:421)
at org.iq80.leveldb.impl.DbImpl.get(DbImpl.java:584) ...

Does anyone know what is going on and how can I fix it? Is it possible to use the old version instead? Thank you very much.
@matthiasblum
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Hi @irislin886,

How many sequences are in your input file? The error seems to indicate that interProScan ran out of memory while holding too much data in memory, and this is often associated with large input files.

@irislin886
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irislin886 commented Dec 3, 2024 •
edited
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Hi @matthiasblum ,

Thank you very much for getting back to me. I have 16 input files that I want to run the InterProScan on. The number of sequences in each file varies from 1501 to 8136. Should I split the input files so each input file contains fewer sequences?

@matthiasblum
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These numbers sounds reasonable.

Are you running InterProScan on a personal device (laptop, desktop), or on a computer farm? How much memory is available?

@irislin886
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I am running InterProScan on my school cluster. I used 1 node, 3 cpu and 20GB per cpu.

@matthiasblum
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Then I would increase the memory (to something like 40GB) and try again.

@irislin886
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I tried to increase the memory but now it showed another error. I removed the interproscan-5.72-103.0 and downloaded it again. This time, I got an error when I tried to run the test command "./interproscan.sh -i test_all_appl.fasta -f tsv -dp". Here is the error message:
23/12/2024 12:16:16:944 Welcome to InterProScan-5.72-103.0
23/12/2024 12:16:16:944 Running InterProScan v5 in STANDALONE mode... on Linux
23/12/2024 12:16:22:906 RunID: tinkercliffs1_20241223_121622420_1u08
23/12/2024 12:16:34:204 Loading file /home/yflin/software/interproscan-5.72-103.0/test_all_appl.fasta
23/12/2024 12:16:34:207 Running the following analyses:
[AntiFam-7.0,CDD-3.20,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2023_05,MobiDBLite-4.0,NCBIfam-15.0,PANTHER-19.0,Pfam-37.1,PIRSF-3.10,PIRSR-2023_05,PRINTS-42.0,ProSitePatterns-2023_05,ProSiteProfiles-2023_05,SFLD-4,SMART-9.0,SUPERFAMILY-1.75]
Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete...
2024-12-23 12:16:41,180 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2023_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2023_05/evaluator.dat -r -s -o ipro /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositePatterns/000000000001_000000000006.fasta
Error output from binary:
bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /localscratch/ps301464-1.tmp /localscratch/ps301464-3.tmp > /localscratch/ps301464-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

2024-12-23 12:16:41,185 [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: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2023_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2023_05/evaluator.dat -r -s -o ipro /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositePatterns/000000000001_000000000006.fasta
Error output from binary:
bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /localscratch/ps301464-1.tmp /localscratch/ps301464-3.tmp > /localscratch/ps301464-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.72-103.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor92.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:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at java.lang.Thread.run(Thread.java:834) [?:?]

2024-12-23 12:16:41,194 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2023_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2023_05/evaluator.dat -r -s -o ipro /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositePatterns/000000000001_000000000006.fasta
Error output from binary:
bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /localscratch/ps301464-1.tmp /localscratch/ps301464-3.tmp > /localscratch/ps301464-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    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.GeneratedMethodAccessor92.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:344)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
    at java.base/java.lang.Thread.run(Thread.java:834)

2024-12-23 12:16:41,195 [amqEmbeddedWorkerJmsContainer-7] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary
2024-12-23 12:16:41,304 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 88 is being re-run following a failure.
2024-12-23 12:16:43,884 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.fasta /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4
Error output from binary:
bin/prosite/pfsearchV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfsearchV3)
Error running prosite binary bin/prosite/pfsearchV3

2024-12-23 12:16:43,884 [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: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.fasta /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4
Error output from binary:
bin/prosite/pfsearchV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfsearchV3)
Error running prosite binary bin/prosite/pfsearchV3

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.72-103.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor92.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:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at java.lang.Thread.run(Thread.java:834) [?:?]

2024-12-23 12:16:43,885 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.fasta /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4
Error output from binary:
bin/prosite/pfsearchV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfsearchV3)
Error running prosite binary bin/prosite/pfsearchV3

    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.GeneratedMethodAccessor92.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:344)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
    at java.base/java.lang.Thread.run(Thread.java:834)

2024-12-23 12:16:43,886 [amqEmbeddedWorkerJmsContainer-4] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2024-12-23 12:16:43,961 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 46 is being re-run following a failure.
23/12/2024 12:16:51:673 25% completed
2024-12-23 12:16:54,792 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2023_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2023_05/evaluator.dat -r -s -o ipro /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositePatterns/000000000001_000000000006.fasta
Error output from binary:
bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /localscratch/ps845307-1.tmp /localscratch/ps845307-3.tmp > /localscratch/ps845307-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

2024-12-23 12:16:54,792 [amqEmbeddedWorkerJmsContainer-8] [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: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2023_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2023_05/evaluator.dat -r -s -o ipro /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositePatterns/000000000001_000000000006.fasta
Error output from binary:
bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /localscratch/ps845307-1.tmp /localscratch/ps845307-3.tmp > /localscratch/ps845307-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.72-103.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor92.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:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at java.lang.Thread.run(Thread.java:834) [?:?]

2024-12-23 12:16:54,793 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2023_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2023_05/evaluator.dat -r -s -o ipro /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositePatterns/000000000001_000000000006.fasta
Error output from binary:
bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /localscratch/ps845307-1.tmp /localscratch/ps845307-3.tmp > /localscratch/ps845307-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    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.GeneratedMethodAccessor92.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:344)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
    at java.base/java.lang.Thread.run(Thread.java:834)

2024-12-23 12:16:54,794 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary
2024-12-23 12:16:54,860 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 88 is being re-run following a failure.
2024-12-23 12:16:56,410 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 1
Command: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.fasta /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4
Error output from binary:
bin/prosite/pfsearchV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfsearchV3)
Error running prosite binary bin/prosite/pfsearchV3

2024-12-23 12:16:56,410 [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: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.fasta /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4
Error output from binary:
bin/prosite/pfsearchV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfsearchV3)
Error running prosite binary bin/prosite/pfsearchV3

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.72-103.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor92.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:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at java.lang.Thread.run(Thread.java:834) [?:?]

2024-12-23 12:16:56,411 [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: python3 bin/prosite/runprosite.py data/prosite/2023_05/prosite_profiles /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.fasta /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositeProfiles/000000000001_000000000006.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4
Error output from binary:
bin/prosite/pfsearchV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfsearchV3)
Error running prosite binary bin/prosite/pfsearchV3

    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.GeneratedMethodAccessor92.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:344)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
    at java.base/java.lang.Thread.run(Thread.java:834)

2024-12-23 12:16:56,411 [amqEmbeddedWorkerJmsContainer-2] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositeProfilesRunBinary
2024-12-23 12:16:56,510 [main] [uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster:190] WARN - StepInstance 46 is being re-run following a failure.
2024-12-23 12:17:00,284 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep:199] ERROR - Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2023_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2023_05/evaluator.dat -r -s -o ipro /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositePatterns/000000000001_000000000006.fasta
Error output from binary:
bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /localscratch/ps480917-1.tmp /localscratch/ps480917-3.tmp > /localscratch/ps480917-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

2024-12-23 12:17:00,285 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:216] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2023_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2023_05/evaluator.dat -r -s -o ipro /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositePatterns/000000000001_000000000006.fasta
Error output from binary:
bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /localscratch/ps480917-1.tmp /localscratch/ps480917-3.tmp > /localscratch/ps480917-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201) ~[interproscan-management-5.72-103.0.jar:?]
    at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
    at jdk.internal.reflect.GeneratedMethodAccessor92.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:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
    at java.lang.Thread.run(Thread.java:834) [?:?]

2024-12-23 12:17:00,285 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
java.lang.IllegalStateException: Command line failed with exit code: 25
Command: bin/prosite/ps_scan.pl -d data/prosite/2023_05/prosite_patterns.dat --pfscan bin/prosite/pfscanV3 -b data/prosite/2023_05/evaluator.dat -r -s -o ipro /home/yflin/software/interproscan-5.72-103.0/temp/tinkercliffs1_20241223_121622420_1u08//jobPrositePatterns/000000000001_000000000006.fasta
Error output from binary:
bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /localscratch/ps480917-1.tmp /localscratch/ps480917-3.tmp > /localscratch/ps480917-2.tmp: Inappropriate ioctl for device at bin/prosite/ps_scan.pl line 1751.

    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.GeneratedMethodAccessor92.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:344)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
    at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
    at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
    at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
    at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
    at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
    at java.base/java.lang.Thread.run(Thread.java:834)

2024-12-23 12:17:00,286 [amqEmbeddedWorkerJmsContainer-6] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPrositePatternRunBinary
2024-12-23 12:17:00,379 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:25] FATAL - Analysis step 88 : Run ps_scan.pl and pfscan Binary for selected proteins for proteins 1 to 6 has failed irretrievably. Available StackTraces follow.
2024-12-23 12:17:00,379 [main] [uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError:42] FATAL - The JVM will now exit with a non-zero exit status.
2024-12-23 12:17:00,379 [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:443) [interproscan-5.jar:?]
java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information.
at uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError.failed(NonZeroExitOnUnrecoverableError.java:43)
at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:169)
at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:443)
12:17:01.115 [amqEmbeddedWorkerJmsContainer-8] ERROR org.hibernate.id.enhanced.TableGenerator - HHH000351: Could not read or init a hi value
org.h2.jdbc.JdbcSQLSyntaxErrorException: Table "KEY_GEN" not found; SQL statement:
select tbl.next_val from public.key_gen tbl where tbl.sequence_name=? [42102-199]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:451) ~[h2-1.4.199.jar:1.4.199]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:427) ~[h2-1.4.199.jar:1.4.199]
at org.h2.message.DbException.get(DbException.java:205) ~[h2-1.4.199.jar:1.4.199]
at org.h2.message.DbException.get(DbException.java:181) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.readTableOrView(Parser.java:7146) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.readTableFilter(Parser.java:1895) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parseSelectSimpleFromPart(Parser.java:2641) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parseSelectSimple(Parser.java:2788) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parseSelectSub(Parser.java:2636) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parseSelectUnion(Parser.java:2469) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parseSelect(Parser.java:2440) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parsePrepared(Parser.java:814) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parse(Parser.java:788) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parse(Parser.java:760) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.prepareCommand(Parser.java:683) ~[h2-1.4.199.jar:1.4.199]
at org.h2.engine.Session.prepareLocal(Session.java:627) ~[h2-1.4.199.jar:1.4.199]
at org.h2.engine.Session.prepareCommand(Session.java:565) ~[h2-1.4.199.jar:1.4.199]
at org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1292) ~[h2-1.4.199.jar:1.4.199]
at org.h2.jdbc.JdbcPreparedStatement.(JdbcPreparedStatement.java:77) ~[h2-1.4.199.jar:1.4.199]
at org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:349) ~[h2-1.4.199.jar:1.4.199]
at jdk.internal.reflect.GeneratedMethodAccessor67.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:385) ~[spring-jdbc-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy30.prepareStatement(Unknown Source) ~[?:?]
at org.hibernate.id.enhanced.TableGenerator.prepareStatement(TableGenerator.java:684) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator.access$200(TableGenerator.java:132) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator$1$1.execute(TableGenerator.java:582) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator$1$1.execute(TableGenerator.java:575) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.jdbc.WorkExecutor.executeReturningWork(WorkExecutor.java:55) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.jdbc.AbstractReturningWork.accept(AbstractReturningWork.java:34) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcIsolationDelegate.delegateWork(JdbcIsolationDelegate.java:57) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator$1.getNextValue(TableGenerator.java:574) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.PooledOptimizer.generate(PooledOptimizer.java:73) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator.generate(TableGenerator.java:570) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:119) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.DefaultPersistEventListener.entityIsTransient(DefaultPersistEventListener.java:192) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:135) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:62) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.internal.SessionImpl.firePersist(SessionImpl.java:804) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.internal.SessionImpl.persist(SessionImpl.java:789) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at jdk.internal.reflect.GeneratedMethodAccessor73.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:314) ~[spring-orm-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy75.persist(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.genericjpadao.GenericDAOImpl.insert(GenericDAOImpl.java:128) ~[generic-jpa-dao-5.72-103.0.jar:?]
at uk.ac.ebi.interpro.scan.persistence.raw.RawMatchDAOImpl.insertProteinMatches(RawMatchDAOImpl.java:37) ~[interproscan-persistence-5.72-103.0.jar:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy96.insertProteinMatches(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:128) ~[interproscan-management-5.72-103.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor92.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:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) [spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) [spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) [spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) [spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) [?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at java.lang.Thread.run(Thread.java:834) [?:?]
12:17:01.117 [amqEmbeddedWorkerJmsContainer-8] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Table "KEY_GEN" not found; SQL statement:
select tbl.next_val from public.key_gen tbl where tbl.sequence_name=? [42102-199]
2024-12-23 12:17:01,122 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:216] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back.
javax.persistence.PersistenceException: org.hibernate.exception.SQLGrammarException: error performing isolated work
at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:154) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:181) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:188) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.internal.SessionImpl.firePersist(SessionImpl.java:811) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.internal.SessionImpl.persist(SessionImpl.java:789) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at jdk.internal.reflect.GeneratedMethodAccessor73.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:314) ~[spring-orm-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy75.persist(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.genericjpadao.GenericDAOImpl.insert(GenericDAOImpl.java:128) ~[generic-jpa-dao-5.72-103.0.jar:?]
at uk.ac.ebi.interpro.scan.persistence.raw.RawMatchDAOImpl.insertProteinMatches(RawMatchDAOImpl.java:37) ~[interproscan-persistence-5.72-103.0.jar:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy96.insertProteinMatches(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:128) ~[interproscan-management-5.72-103.0.jar:?]
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87) ~[interproscan-5.jar:?]
at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118) ~[spring-tx-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212) ~[spring-aop-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source) ~[?:?]
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200) [interproscan-5.jar:?]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073) [spring-jms-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at java.lang.Thread.run(Thread.java:834) [?:?]
Caused by: org.hibernate.exception.SQLGrammarException: error performing isolated work
at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:63) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:113) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:99) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcIsolationDelegate.delegateWork(JdbcIsolationDelegate.java:79) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator$1.getNextValue(TableGenerator.java:574) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.PooledOptimizer.generate(PooledOptimizer.java:73) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator.generate(TableGenerator.java:570) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:119) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.DefaultPersistEventListener.entityIsTransient(DefaultPersistEventListener.java:192) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:135) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:62) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.internal.SessionImpl.firePersist(SessionImpl.java:804) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
... 43 more
Caused by: org.h2.jdbc.JdbcSQLSyntaxErrorException: Table "KEY_GEN" not found; SQL statement:
select tbl.next_val from public.key_gen tbl where tbl.sequence_name=? [42102-199]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:451) ~[h2-1.4.199.jar:1.4.199]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:427) ~[h2-1.4.199.jar:1.4.199]
at org.h2.message.DbException.get(DbException.java:205) ~[h2-1.4.199.jar:1.4.199]
at org.h2.message.DbException.get(DbException.java:181) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.readTableOrView(Parser.java:7146) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.readTableFilter(Parser.java:1895) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parseSelectSimpleFromPart(Parser.java:2641) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parseSelectSimple(Parser.java:2788) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parseSelectSub(Parser.java:2636) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parseSelectUnion(Parser.java:2469) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parseSelect(Parser.java:2440) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parsePrepared(Parser.java:814) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parse(Parser.java:788) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.parse(Parser.java:760) ~[h2-1.4.199.jar:1.4.199]
at org.h2.command.Parser.prepareCommand(Parser.java:683) ~[h2-1.4.199.jar:1.4.199]
at org.h2.engine.Session.prepareLocal(Session.java:627) ~[h2-1.4.199.jar:1.4.199]
at org.h2.engine.Session.prepareCommand(Session.java:565) ~[h2-1.4.199.jar:1.4.199]
at org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1292) ~[h2-1.4.199.jar:1.4.199]
at org.h2.jdbc.JdbcPreparedStatement.(JdbcPreparedStatement.java:77) ~[h2-1.4.199.jar:1.4.199]
at org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:349) ~[h2-1.4.199.jar:1.4.199]
at jdk.internal.reflect.GeneratedMethodAccessor67.invoke(Unknown Source) ~[?:?]
at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
at org.springframework.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:385) ~[spring-jdbc-5.2.24.RELEASE.jar:5.2.24.RELEASE]
at com.sun.proxy.$Proxy30.prepareStatement(Unknown Source) ~[?:?]
at org.hibernate.id.enhanced.TableGenerator.prepareStatement(TableGenerator.java:684) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator.access$200(TableGenerator.java:132) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator$1$1.execute(TableGenerator.java:582) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator$1$1.execute(TableGenerator.java:575) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.jdbc.WorkExecutor.executeReturningWork(WorkExecutor.java:55) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.jdbc.AbstractReturningWork.accept(AbstractReturningWork.java:34) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcIsolationDelegate.delegateWork(JdbcIsolationDelegate.java:57) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator$1.getNextValue(TableGenerator.java:574) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.PooledOptimizer.generate(PooledOptimizer.java:73) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.id.enhanced.TableGenerator.generate(TableGenerator.java:570) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:119) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.DefaultPersistEventListener.entityIsTransient(DefaultPersistEventListener.java:192) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:135) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:62) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
at org.hibernate.internal.SessionImpl.firePersist(SessionImpl.java:804) ~[hibernate-core-5.4.2.Final.jar:5.4.2.Final]
... 43 more
2024-12-23 12:17:01,124 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:218] ERROR - The exception is :
javax.persistence.PersistenceException: org.hibernate.exception.SQLGrammarException: error performing isolated work
at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:154)
at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:181)
at org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:188)
at org.hibernate.internal.SessionImpl.firePersist(SessionImpl.java:811)
at org.hibernate.internal.SessionImpl.persist(SessionImpl.java:789)
at jdk.internal.reflect.GeneratedMethodAccessor73.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.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:314)
at com.sun.proxy.$Proxy75.persist(Unknown Source)
at uk.ac.ebi.interpro.scan.genericjpadao.GenericDAOImpl.insert(GenericDAOImpl.java:128)
at uk.ac.ebi.interpro.scan.persistence.raw.RawMatchDAOImpl.insertProteinMatches(RawMatchDAOImpl.java:37)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy96.insertProteinMatches(Unknown Source)
at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:128)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
at jdk.internal.reflect.GeneratedMethodAccessor92.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:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: org.hibernate.exception.SQLGrammarException: error performing isolated work
at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:63)
at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:113)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:99)
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcIsolationDelegate.delegateWork(JdbcIsolationDelegate.java:79)
at org.hibernate.id.enhanced.TableGenerator$1.getNextValue(TableGenerator.java:574)
at org.hibernate.id.enhanced.PooledOptimizer.generate(PooledOptimizer.java:73)
at org.hibernate.id.enhanced.TableGenerator.generate(TableGenerator.java:570)
at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:119)
at org.hibernate.event.internal.DefaultPersistEventListener.entityIsTransient(DefaultPersistEventListener.java:192)
at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:135)
at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:62)
at org.hibernate.internal.SessionImpl.firePersist(SessionImpl.java:804)
... 43 more
Caused by: org.h2.jdbc.JdbcSQLSyntaxErrorException: Table "KEY_GEN" not found; SQL statement:
select tbl.next_val from public.key_gen tbl where tbl.sequence_name=? [42102-199]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:451)
at org.h2.message.DbException.getJdbcSQLException(DbException.java:427)
at org.h2.message.DbException.get(DbException.java:205)
at org.h2.message.DbException.get(DbException.java:181)
at org.h2.command.Parser.readTableOrView(Parser.java:7146)
at org.h2.command.Parser.readTableFilter(Parser.java:1895)
at org.h2.command.Parser.parseSelectSimpleFromPart(Parser.java:2641)
at org.h2.command.Parser.parseSelectSimple(Parser.java:2788)
at org.h2.command.Parser.parseSelectSub(Parser.java:2636)
at org.h2.command.Parser.parseSelectUnion(Parser.java:2469)
at org.h2.command.Parser.parseSelect(Parser.java:2440)
at org.h2.command.Parser.parsePrepared(Parser.java:814)
at org.h2.command.Parser.parse(Parser.java:788)
at org.h2.command.Parser.parse(Parser.java:760)
at org.h2.command.Parser.prepareCommand(Parser.java:683)
at org.h2.engine.Session.prepareLocal(Session.java:627)
at org.h2.engine.Session.prepareCommand(Session.java:565)
at org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1292)
at org.h2.jdbc.JdbcPreparedStatement.(JdbcPreparedStatement.java:77)
at org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:349)
at jdk.internal.reflect.GeneratedMethodAccessor67.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.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:385)
at com.sun.proxy.$Proxy30.prepareStatement(Unknown Source)
at org.hibernate.id.enhanced.TableGenerator.prepareStatement(TableGenerator.java:684)
at org.hibernate.id.enhanced.TableGenerator.access$200(TableGenerator.java:132)
at org.hibernate.id.enhanced.TableGenerator$1$1.execute(TableGenerator.java:582)
at org.hibernate.id.enhanced.TableGenerator$1$1.execute(TableGenerator.java:575)
at org.hibernate.jdbc.WorkExecutor.executeReturningWork(WorkExecutor.java:55)
at org.hibernate.jdbc.AbstractReturningWork.accept(AbstractReturningWork.java:34)
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcIsolationDelegate.delegateWork(JdbcIsolationDelegate.java:57)
... 51 more
2024-12-23 12:17:01,125 [amqEmbeddedWorkerJmsContainer-8] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:222] ERROR - StepExecution with errors - stepName: stepPfamParseHmmerOutput
org.hibernate.exception.SQLGrammarException: error performing isolated work
at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:63)
at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:113)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:99)
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcIsolationDelegate.delegateWork(JdbcIsolationDelegate.java:79)
at org.hibernate.id.enhanced.TableGenerator$1.getNextValue(TableGenerator.java:574)
at org.hibernate.id.enhanced.PooledOptimizer.generate(PooledOptimizer.java:73)
at org.hibernate.id.enhanced.TableGenerator.generate(TableGenerator.java:570)
at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:119)
at org.hibernate.event.internal.DefaultPersistEventListener.entityIsTransient(DefaultPersistEventListener.java:192)
at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:135)
at org.hibernate.event.internal.DefaultPersistEventListener.onPersist(DefaultPersistEventListener.java:62)
at org.hibernate.internal.SessionImpl.firePersist(SessionImpl.java:804)
at org.hibernate.internal.SessionImpl.persist(SessionImpl.java:789)
at jdk.internal.reflect.GeneratedMethodAccessor73.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.orm.jpa.SharedEntityManagerCreator$SharedEntityManagerInvocationHandler.invoke(SharedEntityManagerCreator.java:314)
at com.sun.proxy.$Proxy75.persist(Unknown Source)
at uk.ac.ebi.interpro.scan.genericjpadao.GenericDAOImpl.insert(GenericDAOImpl.java:128)
at uk.ac.ebi.interpro.scan.persistence.raw.RawMatchDAOImpl.insertProteinMatches(RawMatchDAOImpl.java:37)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy96.insertProteinMatches(Unknown Source)
at uk.ac.ebi.interpro.scan.management.model.implementations.ParseStep.execute(ParseStep.java:128)
at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
at jdk.internal.reflect.GeneratedMethodAccessor92.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:344)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:367)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:118)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
at com.sun.proxy.$Proxy141.executeInTransaction(Unknown Source)
at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1186)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1176)
at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1073)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: org.h2.jdbc.JdbcSQLSyntaxErrorException: Table "KEY_GEN" not found; SQL statement:
select tbl.next_val from public.key_gen tbl where tbl.sequence_name=? [42102-199]
at org.h2.message.DbException.getJdbcSQLException(DbException.java:451)
at org.h2.message.DbException.getJdbcSQLException(DbException.java:427)
at org.h2.message.DbException.get(DbException.java:205)
at org.h2.message.DbException.get(DbException.java:181)
at org.h2.command.Parser.readTableOrView(Parser.java:7146)
at org.h2.command.Parser.readTableFilter(Parser.java:1895)
at org.h2.command.Parser.parseSelectSimpleFromPart(Parser.java:2641)
at org.h2.command.Parser.parseSelectSimple(Parser.java:2788)
at org.h2.command.Parser.parseSelectSub(Parser.java:2636)
at org.h2.command.Parser.parseSelectUnion(Parser.java:2469)
at org.h2.command.Parser.parseSelect(Parser.java:2440)
at org.h2.command.Parser.parsePrepared(Parser.java:814)
at org.h2.command.Parser.parse(Parser.java:788)
at org.h2.command.Parser.parse(Parser.java:760)
at org.h2.command.Parser.prepareCommand(Parser.java:683)
at org.h2.engine.Session.prepareLocal(Session.java:627)
at org.h2.engine.Session.prepareCommand(Session.java:565)
at org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1292)
at org.h2.jdbc.JdbcPreparedStatement.(JdbcPreparedStatement.java:77)
at org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:349)
at jdk.internal.reflect.GeneratedMethodAccessor67.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.jdbc.datasource.LazyConnectionDataSourceProxy$LazyConnectionInvocationHandler.invoke(LazyConnectionDataSourceProxy.java:385)
at com.sun.proxy.$Proxy30.prepareStatement(Unknown Source)
at org.hibernate.id.enhanced.TableGenerator.prepareStatement(TableGenerator.java:684)
at org.hibernate.id.enhanced.TableGenerator.access$200(TableGenerator.java:132)
at org.hibernate.id.enhanced.TableGenerator$1$1.execute(TableGenerator.java:582)
at org.hibernate.id.enhanced.TableGenerator$1$1.execute(TableGenerator.java:575)
at org.hibernate.jdbc.WorkExecutor.executeReturningWork(WorkExecutor.java:55)
at org.hibernate.jdbc.AbstractReturningWork.accept(AbstractReturningWork.java:34)
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcIsolationDelegate.delegateWork(JdbcIsolationDelegate.java:57)
... 51 more
12:17:01.130 [responseMonitorJmsContainer-1] ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Table "STEP_EXECUTION" not found; SQL statement:
select stepexecut0_.id as id1_110_0_, stepexecut0_.time_completed as time_com2_110_0_, stepexecut0_.time_created as time_cre3_110_0_, stepexecut0_.exception_first_chunk as exceptio4_110_0_, stepexecut0_.proportion_completed as proporti5_110_0_, stepexecut0_.time_started_running as time_sta6_110_0_, stepexecut0_.state as state7_110_0_, stepexecut0_.step_instance_id as step_ins9_110_0_, stepexecut0_.time_submitted as time_sub8_110_0_, exceptionc1_.step_execution_id as step_exe1_15_1_, exceptionc1_.exception_chunks as exceptio2_15_1_, exceptionc1_.chunk_index as chunk_in3_1_, stepinstan2_.id as id1_111_2_, stepinstan2_.bottom_model as bottom_m2_111_2_, stepinstan2_.bottom_protein as bottom_p3_111_2_, stepinstan2_.step_id as step_id4_111_2_, stepinstan2_.time_created as time_cre5_111_2_, stepinstan2_.top_model as top_mode6_111_2_, stepinstan2_.top_protein as top_prot7_111_2_, dependsupo3_.step_instance_id as step_ins1_113_3_, stepinstan4_.id as depends_2_113_3_, stepinstan4_.id as id1_111_4_, stepinstan4_.bottom_model as bottom_m2_111_4_, stepinstan4_.bottom_protein as bottom_p3_111_4_, stepinstan4_.step_id as step_id4_111_4_, stepinstan4_.time_created as time_cre5_111_4_, stepinstan4_.top_model as top_mode6_111_4_, stepinstan4_.top_protein as top_prot7_111_4_, parameters5_.step_instance_id as step_ins1_112_5_, parameters5_.parameters as paramete2_112_5_, parameters5_.parameters_key as paramete3_5_ from public.step_execution stepexecut0_ left outer join public.exception_chunk exceptionc1_ on stepexecut0_.id=exceptionc1_.step_execution_id inner join public.step_instance stepinstan2_ on stepexecut0_.step_instance_id=stepinstan2_.id left outer join public.step_instance_step_instance dependsupo3_ on stepinstan2_.id=dependsupo3_.step_instance_id left outer join public.step_instance stepinstan4_ on dependsupo3_.depends_upon_id=stepinstan4_.id left outer join public.step_instance_parameters parameters5_ on stepinstan4_.id=parameters5_.step_instance_id where stepexecut0_.id=? [42102-199]
InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

@matthiasblum
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Hi @irislin886

The cause of the error can be found in the logs you posted:

bin/prosite/pfscanV3: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)

The PROSITE binary requires GLIBC 2.27 or higher, which you don't seem to have. You should contact the system administrator of your cluster and ask them to update GLIBC. Alternatively, you can use InterProScan with a container runtime such as Docker or Singularity: https://interproscan-docs.readthedocs.io/en/latest/HowToUseViaContainer.html

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@matthiasblum @irislin886